Well, I don't necessarily agree on the base-takers' philosophy, I still remember doing it and having fun. And I know a large amount of players like to join in on these missions to go take bases. They shouldn't be shut out because a large number of people on the forum don't agree with the way they like to have fun. That's just my personal opinion. 
Sorry about the 'lolmeh' bit, it was the only thing I could think of at the time (excuse: was cold and just woke up
). I agree with what you said about getting enjoyment from that part of the game, but I'm honestly not sure how having three uncap's around the HQ would help. Perhaps a solution could be to make
most of the bases uncapturable, but leave TT (or its equivalent on a given map) capturable. If so, you would allow for the TT bases to switch hands, thus giving the base-takers something to work at, whilst the HQ would give other players an objective to destroy (and provide a target for the big bomber missions), and the rest of the map could be used for base to base combat.
Here's an idea of what it might look like:
