I think most maintenance needs to go away. Have buildings use strategic resources more often, and double or triple the number of buildings. That makes it so that you always have something to build and specialization happens because you literally can't build everything, but you can build the things you need for a given purpose -- and it hurts ICS a bit because if the buildings use resources and are really good, then building a bunch of small cities sucks more. I think the game needs more buildings like the Mint, which increase the value of resources or other tiles. It doesn't need any buildings like the Monastery or Circus, which requires a resource but doesn't require that you work it -- that makes the resource great for overlap between cities (3 cities near the same horse can each build a circus for happiness).
I don't think Trade Posts are OP. The problem is everything else is far too weak, making money the preferred way to handle everything. Up the value of production, make city growth a lot easier so you can have big cities, improve the not TP improvements and add some more and you'll have a much better system. I think some of the things in Civ IV need to come back here. Workshops for instance let you adjust to a bad tile situation (where you needed a production city but had too few hills). The ability to adapt is really nice there. Perhaps similarly special resources should have multiple ways to cultivate them (or perhaps just enhancement buildings is the way to go there).
I do think something needs to be done about the military though. I think a lot of the production fixes will end up being weird with small militaries. I don't like the idea of going back to SOD, but a CTP2 system would be pretty awesome (units stack up to 12, can form armies that use combined arms and attack as one).
I definitely agree with you that buildings need to use resources more, that's a very clever idea.
I don't think this necessitates the elimination of per-building monetary upkeep.
As I said before, it's a strategic decision.
I think good retrofitting needs to tie every feature with other features more favorably to produce a rich matrix of possible strategies, none 'perfect' and all tailored specifically to a situation.. removing a game system outright I don't see as a good solution simply because it detracts from the possibilities.
Back when I was modding for fallout3 (made a few mods, including "Welcome To The Wasteland") this was my working philosophy when other modders just wanted to cancel out everything and make it like fallout2.
For example, what if I want to run a negative economy just to get the benefit of certain buildings for a set amount of turns until I sell them? Or more simply, because I anticipate large economic growth as part of my strategy?
Ideally you should always have a choice that is good situationally but can backfire
Regarding military/production:
Tried playing with the mods that increase strategic/food/mine yields?
I think you'll find the experience much improved. And also much more akin to civ4.
Also, the AI seems to react very favorably to these changes.