Fable, it sounds like I should try to print down the number of beds in the houses (when I know about this, of course).
I can tell you that within a few weeks I will release an upgraded version of my Aleswell Home, where you will have totally five beds (so if your char sleep in a chair, there will be enough beds for five companions

).
Sometimes, using housemods together might be a solution. I love Khettiennas Amenthala's Well House but it only have two bedplaces. But, I also have my own Waterlily Cottage on the other side of the road (not conflicting at all) which also provides two bedplaces - i.e. a perfect "extra house" for Amenthala residents.
I do use something of a combo: Tchos Alchemy Tower for the companions, and the Armory Lab Revised for mannequins, weaponry, armor, etc. I could link them in the construction set, but it's easier (and more in-game) to use a Mark/Recall via Supreme Magicka. I know that isn't what you mean, but having two houses would make one not feel "lived in" as a base of operations. But if I could find two mods that allow for, say, 5 companions a piece...
Still, I always look around for new houses with the hope of finding something that offers:
1) A lot of beds for companions, and lack of access to rooms where they could pull a Constance on my goods.

2) A nice magical area, complete with enchantment/spell creation, and a COBL potions/ingredients area.
3) Good armory/weapons display, and plenty of room to display mannequins.
4) A nice library. I like it stocked, because it's next to impossible even using the mods provided to put up books properly in Oblivion, but that's secondary.
5) Creativity, very in keeping with the game world.
Other than that, I don't have any requirements.