I feel like a base in this game should definitely be something special in the sense that everyone should have a main or signature base and although the overall feel of a base can define it I think that there should be more base bonuses. With that being said I'm going to throw out some base bonus ideas but please feel free to post your own and make comments on mine.
I think it would be cool if there were 2-3 bases around the map that would allow you to train a hero regardless of rank if you based there such as Shadow sniper ( lots of noobs aren't even rank 7 and being able to at least play some other heros they haven't been able to use could encourage them to start saving their codes even though it only takes a second.. ) Commander and astronomer with each of these being exclusive to the base so Shadow sniper but not commander or Astronomer being able to be trained at one only commander at another and only astronomer at another. I think it would encourage people to learn new bases if it meant being able to use a higher rank hero
It would be cool if the fountain in the gathering hall gave off mana regeneration or something so that people who claimed the alchemist in the mailroom could possibly base there while having increased mana regeneration for this claimed alchemist. I feel like that could make that a more popular base if that were an available bonus.
Since black larcenies have been nerfed in the 6.43 change log maybe have a black larceny spawn in one of the cages in the torture chamber at the 26 or 28 minute mark. ( if claimed )
A bonus where an alien type egg spawns in either the middle or one of the corners of that base and when you claim the base it starts to hatch over a period of a couple minutes and when it hatches you can either get 3 repair bots, an alchemist or a tiny level 3 lumber mill item ( random every time )
Let me know if you liked my ideas and feel free to leave some ideas of your own