I recently watched Devstream #36 where they discussed the possible implementation of the fan created 'Focus' concept (http://warframe.wikia.com/wiki/Focus). They discussed how the 'lenses' or some such were to be added and how specicialisation benefits were to be made from them. They did, however state they were struggling to find benefits that werent mod-like or warframe power-like. I also read the fan blog of the implementation of Warframe specific auras that added some passive bonus (https://forums.warframe.com/index.php?/topic/227175-the-ballsiest-idea-ive-got-warframe-passive-abilities/ ). This idea seemed to me quite interesting. As such, I thought of a pretty 'balls-to-the-wall' idea where these two can be combined. However, it does go back on a lot of already thought of and most likely coded stuff that's already aimed at being in U15.
If all Warframes were to be split up into three categories (Holy Trinity or some such: Tanks, Supports and Damage dealers) and thus each group attributed to some Great House (insert lore here). Then one would choose at some stage which house to be aligned to and these would make it possible unlock the auras for all the Frames which fall under that House. Focus exp would then go to unlocking every Frame's passive aura by playing with said frame. Still not sure about whether one should be able to then swap Houses, but if you could, it should be expensive.
Though its' very abstract and most likely far out, I think this idea would create an interesting way for one to specialise in a role for your entire profile and also add some more endgame specialisation.
TL;DR: Warframe specific passive Auras + Focus system = End Game Specialisation of Warframe Profile in some Holy Trinity-esque manner.