I don't hate against clones, the reason they made em in, was that it's a lot less balancing, bug fixing and program work to whip out a clone then a completley original skeleton and moveset. I mean sure I would prefer all original characters but I think the reason so many made it in was that it was just less work and I'm grateful for all the characters I can get (save for pichu. WHY oh why?). It is quite obvious in the time they had a decision was made to start cloning characters and save on production time, this is why G-dorfs sword never made it in and the clones got the same movesets and skeletons. If you say no clones, they woulda had to drop 6 characters and definatley woudln't have been able to add 6 unique ones.
but maybe I'm biased as I somehow main 3 of the clones
my biggest niggle was balance which has been beaten to death, and lack of custimization in all the special melees. The one thing I would say about balance is that of course balance wasn't perfect on release as most of the metagame and tech just hadn't been discovered or perfect and hence wasn't a big deal, plus it's even more complex to balance the tournament level metagame and keep the scrub/noob level balanced as well. I think that the only way the game could be balanced would be continual reviews and patches much like Halo or world of warcraft. Balance has always been a big issue and I've been a tournament player in it. However Blizzard makes an honest attempt at balance and had character reviews for 2 years straight constantly sorting bugs, tightening gameplay and balancing character mechanics.
I would be happy with even a little more balance aka 13 or so characters being tournament viable, or just smaller disparities in certain matchups but with such a big roster I doubt that will be possible