The best Transformers fanfic I've read is based in the 2007 movieverse and called 'Naturalized' by An Cailin Rua/Tricolora. It's still the ONLY Transformer fic I've ever felt moved to comment on when it first started running over on the fanfiction dot com site and it's one of the few I've seen that's written on a fully adult level and which features Transformer characters that are relatable yet seem non-human. Unfortunately, it's no longer up on the internet, but a fellow-fan who evidently admired it even more than I did took it upon herself to restore it (with the author's permission) and make it available again via email. Here's the link--you can check out the summary and maybe it'll be the sort of thing you're looking for...:
http://tf-fic-squee.livejournal.com/20199.htmlI also have very fond memories of a series of Beast Wars Dinobot stories I read years ago written by a German fan which were also very seriously done--angsty character drama type stuff--but those were hosted on a private archive. If you like this character and want me to, I'll try and track them down too...(if they're even still available)...
I've used BW Optimus Primal myself in a Trek fic--he's there so I can contrast his leadership style with Captain Sisko's--but I dunno...it's not really his story. However, on the plus side, I do write him seriously and serious versions of Optimus Primal are hard to find. (I've looked...) If you're really keen on him, I guess I could pull his scenes, rewrite a touch and put them over on the fanfic forum so you'd have at least a bit of fic about him that isn't goofy or childish or just plain smutty...can't guarantee the
quality, just that Primal won't be goofy, childish or smutty...
Any other fics I can think of that I'd consider both good and memorable all seem to involve G1 Megatron whaling on Starscream and having highly unprofessional relations with him. Probably NOT what you're looking for, I'm guessing...