The reason why I made mention of minis initially was that Thundershot made mention of squares, facing, and reach beforehand, which usually means minituares (or at least counters). My main point, however, is that BESM D20 follows a different philosophy in regards to combat and roleplaying in general. Their approach is much more abstract and cinematic, which is appropriate towards those running an anime-centric campaign. Their approach also tends to de-emphasize combat by bringing it up only when necessary.
Of course it doesn't exactly mesh well with standard D20. That's because it's another take on D20 aimed more towards those who want more cinematic mechanics. It's not perfect (my major gripe is that character defense is insufficient at the higher levels), but it's not a bad system for what it aims for.
As for the issue of replacing feats with skills in BESM D20, it actually makes sense if you're playing a campaign that's anime-centric in nature. In a lot of anime, you have characters training themselves to get better at a particular combat style (martial arts, swordmanship, marksmanship, etc.). BESM D20 approaches this by using a combination of skills and attributes, both of which can be ranked. With feats, it's a matter of having or not having the appropriate feats. With skills and attributes, you may have either one or both, but other characters may be better or worse at it, and you can improve at either at a much more incremental pace.
If you prefer standard D20 mechanics, the authors tell you flat-out that you can switch back. It takes a bit of work, but it can certainly be done. They may prefer the use of BESM D20 mechanics (after all, they wrote the book), but they aren't the gaming police and would prefer that players and GMs have fun rather than strictly adhere to one or the other at the expense of having fun. If you have more fun with standard D20, then by all means use it.
As for the matter of rule-breakers, min-maxers, and munchkins, it's the GM's responsibility for dealing with them. The GM can either deal with them appropriately or let them run amok. It is not the game system's responsibility to keep them in line. If I had a group of players who tend to abuse rules, I'd lay down the law or look for another group that isn't a hassle to deal with. Either that or put them through a few sessions of Paranoia.
