There were plenty of G1 references in season 1 of Beast Wars. It wasn't all in season 2 and onward. We had Waspinator thinking he was Shrapnel for a bit and Blackarachnia explaining to Megatron who Shrapnel was. Of course there was also Starscream.
As for comics vs cartoons, I always sided with cartoons, but that's primarily because the cartoons were all I knew as I never read the comics.
As for the origins of the Vok, they were never given any in the show so I pretty much disregard what was said in interviews with the creators/writers well after the fact, as they've reported other info inaccurately in such interviews, not that I can blame them given how much time had usually passed between them actually working on the show and said interviews etc.
Anyway, I'm both happy and quite surprised to see Beast Wars getting all the love it is lately, including the inclusion of several actual Beast Wars figures in the Thrilling 30 line for Generations, especially since they're being called Maximals and Predacons, not Autobots and Decepticons as has often been done with them when integrating BW characters into newer lines.
I agree with the overall sentiment that I'd like to see more re-creations of the Beast Wars characters with the toys being more show accurate using modern engineering. I believe we're in the sweet spot of virtually all of what we saw onscreen being possible, especially when I look at Generations and the Masterpiece line. I think Hasbro and Takara are clearly well aware now that us Beast Wars fans aren't going anywhere and that even though there are way more G1 fans, there are still enough Beast Wars fans to warrant throwing some love that way. To me, Beast Wars was always the continuation of G1 and since I grew up with G1, seeing it while in my late teens/early 20's on TV was like being a kid again.
I too have always hoped for a Beast Wars movie based on the show (as part of the show's continuity, not a reboot/retelling of it or anything, although that would be cool too
) and I'd also love a series/movie/something that really filled in the gaps between the end of Generation One and the beginning of the Beast Wars. If Hasbro could get the original series creators/writers for Beast Wars to do such a thing, that would be the greatest of all. To see those characters and hear those voices again in something new would be so sweet.
Either way, I'm thrilled to see Beast Wars getting so much attention lately and I hope that these Beast Wars commemorations and nods (like Beast Hunters, the Thrilling 30 figures, the comics etc.) do very well so that Has/Tak might be more inclined to do more stuff like this going forward. I don't want Beast Wars nostalgia to completely drown out G1 or any other continuity/toyline etc., but I definitely want to see it continue to be a part of what the Transformers brand has going on.