The answer to this question is both complex and simple, complex because of personal tastes and such, simple because it should be obvious from the get go.
All Of Them!!!
However, to narrow it down a bit we shall discuss a few that others have omitted.
Claw Jaw: A Maximal Squid who was PINK, he would have been an interesting character to see incorporated into the first season's dynamics simply because we never got anything under water until Season Three. And Aquatic Beast Wars characters were both quirky looking and fun.
Snapper: One of the all time coolest looking figures in the Basic size class, I mean this guy was a combination Slash from TMNT and a Transformer. What's not to love about him? Plus if memory serves his bio hinted at piratical nature, just avoid stereotyping him and he could have been a great wild card to throw in.
Insecticon: Personal fav of mine, nothing more.
Jetstorm & Retrax: While I was collecting the BW Era figures, during retail days of time long past, I always went for the non-show characters because of how cool they looked and how fun their bios made them out to be. (Also it was difficult to find Tarantulas, Waspinator and Black Arachnia after a while.) This terrifying looking duo of Predacons were made into Cybertrons for Beast Wars II in Japan by Takara and called the Insectrons... Or something to that effect.
But their Predacon counterparts from across the sea were much more evil looking and would have been great foils for some of the on-show and non-show characters.
Plus, throw in Manterror and you would have had the unholy trio of doom, with one dude (Retrax) who enjoyed making homes and traps in numerous tunnels and filling them with the body parts of deactivated Transformers. Another dude (Jetstorm) who could almost be like a ninja in the way he was portrayed in his bio (if memory serves) and the third member (Manterror) being the over-the top villain who constantly refers to himself as The Manterror (Like some kind of Predacon Wrestler or something.) Even his bio started off with the line The Manterror blah, blah, blah.
Transquito: This dude got a lot of flack back in the day, he was a non-show shelfwarming monstrosity who couldn't be given away for the kiddies or fans alike. Unless you happened to dig his look, and I did in fact do just that. Transquito was a terrifying menace capable of driving his enemies insane by just biting them. Plus who didn't want to see a ten foot long Mosquito flying around on the show?
Powerpinch & Drill Bit: More insect based characters might have made things a tad one-sided when it came to the six legged menaces, but most of the first two years worth of non-show Predacons involved insect based beast modes. And an army of insects swarming the Maximal base would have been awesome fun to watch. (Even if they killed them off after a major three-part epic or something.)
Bonecrusher: Mainframe could more than do better using this character compared to what Takara gave us in Bighorn from BW II.
Noctorro, Air Hammer & Bantor: These three quirky looking fuzors would have been fun to watch. Great looking robot modes, insanely awesome fuzed beast forms. What's not to love?
Sky Shadow, Buzzclaw, Terragator & Injector: While the Maximal Fuzors were quirky and fun, the Predacon one's had menace and danger added to their repertoir. (And had Injector been on the show maybe he wouldn't have pegwarmed so badly.)
I could go on, but I think we should leave it here for now. Besides I'm running low on characters that could be left off of this list.
Beast Wars was one of those cartoons that might have been funner with a bigger budget, a larger number of episodes per season and an extensive cast. But we may have sacrificed some of the poignant character moments in favor of G1 toyline catering syndrome had we gone that route. Still, it's fun to imagine what if.
I kind of wish that IDW would attempt a new BW Comic series revival, that instead of tying itself to the old cartoon series, takes the characters and re-tells the story with more characters, and more emphasis on being less tied in to the typical Unicron/Energoise story arc.
I really think BW Would lend itself well to a re-telling in comic form, perhaps involving the original show creators who could take the series in a much broader direction.
Introduce the new characters at a much more reasonable pace.
