Either implement a conquest battle mode, or simplify things and spawn MOTF 30 seconds into the round (so infantry can fight over an area, and try and take and hold it).
This. I forget who I originally saw suggest this (I think it was Xeen), but making MoTF spawn early in the round would solve a lot of issues in battle. Some people run off into the corner and do nothing all round? Doesn't matter, the game ends without them needing to die. Bunch of people holed up in an easily defensible location? Again, doesn't matter, unless that location is actually on the flags. Some HA/HX kiting in a 1v15 situation? Doesn't matter, unless he's holding the flags.
Right now, the best solution to people holed up in a defensible location is to do absolutely nothing for several minutes in a row, until MoTF eventually spawns. People either have to choose between having fun, or winning. I'm stubborn, so I prefer to wait for the MoTF just to spite the other guys (even if we have 30+ people and it's just a single enemy). It is also incredibly frustrating to throw myself into a meatgrinder along with a handful of teammates in a last-ditch effort to do enough damage to eke out a win, just to die and see that there are a chunk of well-armored friendly infantry hiding in a corner so that they can score some kills before we lose.
The only issue I can think of is that MoTF spawns would all have to be balanced so that both teams both have equal access to them.
e:
The radius and cap time of the flags would likely have to be increased to accommodate high player counts. There are also a whole slew of interesting balance tweaks that could be tried - for example, weighing players close to the flag heavier than players who are at the extremity of the cap radius.
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