I'm a little torn between the two.
Siege is always fun. You can jump in with a bunch of random people, defend some castles and move on. Having a quick respawn and lots of players makes for some intense fights, and having a relatively short timer per round means the maps are cycling and things can be pretty much left on autopilot. Siege is more or less stable and working as intended.
Invasion is also extremely fun, but the pacing can get really out of whack. When you have a coordinated team and a plan, you can tear through some things and its all great. When your team isn't as coordinated, or you have some players who don't really know whats going on, you can whipe really quick and it's frustrating to play the same 4 or 5 rounds over and over. It's also tedious to have to wait until every boss round to respawn, watching that one last guy alive running in circles on a horse hoping to kill 25 hammerzeits (though that was awesome with the horse archer last night.) I don't know how many bugs or whatelse exist in the Invasion mod.
The real upside I can see about having a dedicated Invasion server is people getting practice. The more exposure players have to the mod then the better they should be and the likelyhood of seeing the later rounds would increase. Plus, your sever's population limit adds for an interesting dynamic that the other Invasion servers with lower pop lack.
So considering all of that, if I had to choose I would argue for Invasion, at least for the time being. There are a lot of Siege servers, but not many Invasion, and having you clan tag on an Invasion server seems like it would be good exposure for the mod, thus increased player skill and the chance to find more bugs or things that would work better so the creators can polish up their product. The only thing that is really holding me back from a definitive answer is the respawn. Right now with your battle server you have the realistic, one death and your out, while your siege is more crazy kill kill relaxed. If you screw up you can still play and have fun. Whereas, if you were to have a battle and an invasion server people could only play on ATS servers in short bursts and, if their skill is anything like mine, would spend a lot of time floating around in spectator mode. (Here's where you tell me to l2play nub

)