lots of stuff...
but i guess the most important stuff would related to pvp/bvb and a lack of variety in both modes. i feel like the things that would fix most of these problems would be the following:
-have a stat cap for pvp/bvb so the stats of armor with both primary and secondary stats get rounded down to whatever level bladess/cpu/rapid impaler +7 is... this will fix your problem with an RT1/2 patch owning the base in 5 hits, and players with this armor still get the insane stats for sector mode. this also doesn't prevent these players from entering a no op items tag room.
-if it is possible, make it so II skills do I skill damage (ie upper II does upper 1 damage) so there is no need to use an op tag and limit the number of players that enter your room
-fix merc drop rates to make base more strategic*
-adjust the stats of some mercs*
-remove TG as a stat from e.f.s and minibots and replace TG with HP (so a +4 e.f./minibot would have HP, crit, and sp)
* = don't do this without someone who is an expert
these are my 2 cents. if you don't want to do this stuff, that's your decision. however, i believe these things will make bc much more enjoyable and you might get some of your older players back.