Let me explain some pros and cons of F1 hybrids, and pros and cons of open-pollinated varieties.
Pros of commercial F1 hybrids:
- They are supposed to be at least as productive as the most productive parent of the cross (or so I've heard). This doesn't mean either parent was particularly productive, however (although productivity is probably something the breeders of commercial F1 hybrids generally look for). So, F1 hybrids aren't always more productive than open-pollinated varieties (even if it may frequently be the case).
- They often have what is called hybrid vigor.
- They are generally bred to be tolerant to some diseases.
- They generally have the backing of companies that may do a lot of research in their breeding (as well as their audience), and may actually do the tests to make sure they're disease tolerant.
Cons of F1 hybrids:
- Often isn't always. They don't always have hybrid vigor. They don't always resist the specific diseases in your garden (even if they are tolerant to loads of other diseases). They are not always very productive. For instance, one F1 hybrid might do great for you every year, but another F1 hybrid might never do very well (or it might require different treatment to do well). One F1 hybrid might be well-adapted to your growing conditions, and another might be more suited to another region. The same is true for open-pollinated varieties (perhaps to a larger extent), but F1 hybrids are not excluded (this is my experience; for instance, with tomatoes grown in my yard, Bush Goliath F1, Park's Whopper F1, Early Harvest F1, and even Lemon Boy F1, were all extremely outperformed by Roma, Yellow Pear, Matina, Thessaloniki, Sweet Orange Cherry and others).
- They don't breed true (much how mongrel cats can have all sorts of offspring in one litter). So, if you save your seeds and grow them again, it is improbable that you will get the same thing. It is possible that you'll get something that seems the same (but genetically speaking, it would be very unlikely for it to actually be the same). There are a lot of things you have to account for to make sure it's sufficiently the same (e.g. resistance to every one of the diseases/pests, days to maturity, fruit shape/size, productivity, taste, texture, number of seeds, leaf type, epidermis color, flesh color, etc.)
- You won't get the benefits of acclimatization to your growing conditions (e.g. climate, kind of soil, pests, diseases, etc.) via seed saving. Although it is possible that the parent stock are grown in similar growing conditions (but finding out may be difficult, unless you make the hybrids yourself).
- You generally have to buy them. You can create your own, however.
- You don't always know what the parents of the hybrid were (so, that makes the F2 hybrids even more unpredictable).
- They're not known for their taste, usually. However, there are some F1 hybrids that are (such as Sungold F1 tomatoes, Sunsugar F1 tomatoes, Ambrosia F1 melons, Flavorburst F1 peppers, and such). If your friends are picky, they might not eat hybrid produce, but I don't know that this is a problem for most people.
Pros of open-pollinated varieties:
- They generally breed true.
- You can have the benefits of acclimatization through growing in your garden's conditions over and over again.
- Some of them are very productive (although you may have to do some searching to find them): e.g. these peppers: Neapolitan, Corbaci, Ring of Fire, Orange Carbonero, and Chervena Chushka—and these tomatoes: Matina, Roma, Thessaloniki, Yellow Pear, Red Pear, and Sweet Orange Cherry. Which ones produce the best seems to depend a lot on your growing conditions, too, though (i.e. soil, humidity/aridity, temperatures).
- It's often easier to find unusual varieties that aren't hybrids (the reverse may be true for species where hybrids are less abundant, or where they take a long time to get fruit, and thus take longer to breed, and longer to stabilize after hybridization—e.g. oak trees). F1 hybrids are generally created by commercial entities, who want them to sell to the masses (not just to people who like cool stuff). That means a high portion of F1 hybrids have well-known traits that won't surprise people (such as red, round tomatoes). All kinds of people breed open-pollinated varieties. So, you get some interesting stuff with them, more often, in my opinion (you might get such as fuzzy, white-skinned, striped, oxheart tomatoes with wispy, chartreuse foliage, anthocyanin on their fruit skin, and bicolor white and brown flesh—I don't know a tomato like that; it's just an example of something you're a lot more likely to see with open-pollinated varieties, because companies that make F1 hybrids seem to know that a lot of people just want regular red tomatoes, and they won't easily be persuaded to eat anything else; nevertheless, unusual tomatoes do have their followings, and sometimes you see unusual F1 hybrids, too). For examples of unusual open-pollinated varieties, check out tomatoes by Brad Gates and Tom Wagner.
- Open-pollinated varieties are more likely to be fertile. Some hybrids are sterile on account of chromosome differences of the parents, or they might have cytoplasmic male sterility (CMS) bred into them for commercial purposes. You're unlikely to find sterile F1 hybrid tomatoes and peppers, though, but obviously, you have such as seedless watermelons (one method of making them requires hybridization between a diploid and a triploid, which is supposed to produce sterile F1 hybrid offspring).
- You can find very vigorous open-pollinated varieties, too (however much research it takes to find them; e.g. Sweet Orange Cherry tomato).
- There are open-pollinated varieties with lots of disease-resistance, too (e.g. Walter tomato, Atkinson tomato, etc.)
- You can often get open-pollinated seeds for free with a SASE (and/or for trade) from nice individuals online. In fact, some of the newer varieties aren't even available for sale.
- It's a lot easier to find reviews and information about open-pollinated varieties than it is for F1 hybrids. This is probably due primarily to the price difference, and the lack of seed sharing with F1 hybrids.
Cons of open-pollinated varieties:
- Not all heirlooms and other open-pollinated varieties are known for their taste (especially early and productive varieties, although those generally taste pretty good in my garden). For instance, a lot of people aren't fond of Yellow Pear tomatoes (although Yellow Pear is not early). Some people love it, though. Usually, it's the mid-season and late-season heirlooms that are stereotypically known for their taste (e.g. Brandywine tomatoes).
- Although there are a good number of productive, open-pollinated varieties, you may have to do a lot of research to find the right ones for your growing conditions.
- Some of the disease resistance may be anecdotal, rather than officially researched. University-bred open-pollinated varieties are probably more likely to be researched in this regard. Verified disease-resistance is generally much more common in F1 hybrids. However, open-pollinated varieties should have two alleles for a particular disease-resistance gene, while F1 hybrids may only have one. So, if you find open-pollinated varieties with verified disease resistance, it may be more highly expressed than in some F1 hybrids.
- Vigorous plants seem to be more common with hybrids.
It should be noted that you can buy F1 hybrid seed that is less expensive than usual, but that depends on where you buy your seeds. Buying in bulk at some stores may be more affordable (if you need bulk quantities).
So, to answer your question, it really depends on what you want and how much research and experimentation you like to do. If you don't like to do a lot of research and experimentation, if you don't want to save seeds, and if you just want disease-free, prolific, vigorous plants that produce what people generally expect them to produce, then buying tried and true F1 hybrids is probably what you'll like the most.
If you don't want to rely on companies forever, if you want to save seeds, if you like large numbers of unexpected varieties, if you want the benefits of acclimatization, if you want to impress taste aficionados (or if you are one), etc. you might try open-pollinated varieties. However, if you're just going with a small selection of open-pollinated varieties in a single store, they're likely hand-picked varieties, most of which are capable of doing well in your area (or else are so popular that people buy them even if they don't do well), and there might not be as much of a difference in the success rate between those particular ones and the F1 hybrids they also sell (but the F1 hybrids will still probably perform better most of the time—though not all the time—in those cases), and you likely won't often find very unique open-pollinated varieties in your average offline store (don't count on finding fuzzy, white, striped, multiflora, oxheart tomatoes with anthocyanin on them, and chartreuse foliage; you generally have to look online to find anything with any of those attributes).
All in all, the answer really depends on which F1 hybrid or open-pollinated variety you're talking about, and how you intend to grow it. But, more importantly, it depends on what you like.
You probably won't find any statistical difference between germination in F1 hybrids and open-pollinated varieties you buy in the store. They should be about the same (if the same company sells them). However, if you want great germination, seed-saving should help there. I've found that seeds I save myself germinate faster, more vigorously, and more often than those I buy or receive from someone else. I know at least one other person who has said the same.
It should also be noted that there are other tricks you can do to improve your results (beyond the choice of F1 hybrids versus open-pollinated varieties, soil amendments, watering and stuff like that). I've heard about companies cold-treating seedlings in a certain way that is supposed to help them produce fruit sooner. I've also found, personally (so consider this anecdotal) that Morelle De Balbis seeds frozen in the fruit did better post-germination than those that weren't frozen (the plants were bigger, more productive and more vigorous, although germination was delayed, and germination rates declined). There are also plant regulators (i.e. hormones) that may impact matters.
If you want to keep your F1 hybrids around without buying more seeds, you can overwinter your plants, and/or take cuttings to overwinter for next year (just make sure they're not diseased). Cuttings will have the right genetics. Methods to preserve the true F1 may vary from species to species.