I very rarely visit the forums so not sure if any of these idea have been suggested before.
Auction House - An upgrade for the provision house, maybe using ewp and granite (note not excessive amounts, no more than 1k of each)also not upgrade-able with gems. After doing this upgrade you can auction off your excess materials to the highest bidder for the material of your choosing, here's the catch though, it is a silent auction and nobody can see the other bids and you can only bid 3 times on each auction. Auctions to last just an hour or two and you can only post a few auctions per day. All items should be auctionable including gem gifts and the cost is taken direct from your stores at time of bidding. There should be no limit on the amount you can bid. Hopefully this may put an end to so called "scammers". Obviously the item would need to be in your stores or star menu. Imagine being able to auction a maxed lonely marble block! Only created settlers from bread would be immune to auctioning.
Mayors House - After upgrading maybe an increase in either pop limit or settler spawn rate along with the increase in stores. I'm not talking massive numbers maybe an increase in pop limit by 10 per level so a maxed MH will only give an additional room for 40 settlers. As for the spawn rate I think a decrease by 1 minute per level should still keep the game at it's nice sedate rate.
General Exp - The more a general battles and wins the more exp he gains and can level up just like the player. Say for every 10 levels he can command an extra 10 troops in his army, Maxed out at 50 of course but that would mean by that point he would have gained 500 levels. Would only apply to the reg gen of course. My thinking behind this is to reduce the reliance on guides for adventures and make players think more creatively, also it shouldn't lower the value of the vet gen due to the high amount of exp needed to reach that level.
Stack-able Buffs - I'm not thinking of being able to spam a building with dozens of buffs to keep it permanently shiny. Just 2 or 3 max and only on your own island. This would hopefully still make it worthwhile to buff each other regularly. Also the limit for buffs could be at baskets to keep the sale of gem buffs viable.