The Reapers basically "guided" evolution, according to the info I've seen in-game and elsewhere, which suggests genetic manipulation. It's doubtful they "seeded DNA" in the sense that they did something major planet-wide, but more likely that they genetically modified certain individuals and/or encouraged them to breed. The Protheans may have involved themselves with some species, but most were Reaper-influenced.
It's doubtful that species can interbreed with anything other than asari--and asari can only do this because they don't mate in the traditional sense; they have no gametes. The genetics are too different. Salarians are egg-layers with multiple births; humans and turians don't have the same chirality; krogan have mass births like salarians but they don't lay eggs. How the biology works does actually matter in terms of whether or not you could successfully breed with another race. Not only that, but, for instance, drell are a totally different genus from humans--drell are reptiles, humans are mammals. And nothing can truly hybridize with the asari, who can only mate mind-to-mind without joining gametes; any breeding they do is strictly randomizing genetics that already exist within the asari format (to which end it's surprising to me that they can't reproduce without mating at all--parthenogenesis would actually make more sense because they are all female).
Even if some species can interbreed properly, as in sharing gametes rather than "scrambling DNA" as the asari are supposed to do, the resultant offspring isn't likely to survive due to complications of how their basic internal organs function. And then there's what Shepard says at the end of ME3 to Garrus, if you romanced him. He talks about having children together, and Shepard points out that it wouldn't be biologically possible--which indicates that Shepard has already learned that human/alien relations are not going to result in children (though the chirality thing would be an even bigger barrier than just being different species). Remember, you'd be closer related to an earthworm than you would be to most of the ME3 aliens. It's an interesting theory, but I just can't see it actually panning out.
The reasoning behind it was that mostly species that fit into the bipedal, relatively humanoid template could adapt to the template of the machinery seeded by the Reapers. The rest were mostly uplifted by the Council (i.e. the elcor), or in the case of the hanar, by the Protheans. You'll notice that we also only see one methane-breathing species (or was it chlorine?), the volus.
It's entirely possible that other species developed in an entirely different way, perhaps in another galaxy, without the guidance of the Reapers. There may be squid- or octopus-like aliens somewhere else. It's also possible that there are other intelligent creatures that flew under the radar because the Reapers were looking for "bipedal humanoids." What if the "shifty looking cow" is actually a sentient, sapient creature?
Oh, and I forgot to add, didn't I read in some codex entry, book, or something else Mass Effect related, that it's actually illegal to manipulate species' dna to make hybrids? Which doesn't mean it never happened in the past, but it does mean that we won't see human/salarian hybrids anytime soon.
But in terms of design, I'd say that the Bioware team developed most species as humanoids because it's easier to code them and animate them in combat that way, and also much easier for us to identify with human-looking characters than with some completely alien-looking monstrosity.
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