On dupes, I think the problem is similar to the problem with blood clotting in the human body. Something like three out of four of us will die because of some problem with blood clotting (not clotting when bleeding or hemoraging, clotting at the wrong time with heart attacks and strokes). This one bodily system is vulnerable to several problems at the same time, but these problems are mostly the same problem (blood clotting is a very carefully balanced system that only really works in a small window). Think of the UO database in the same way. The original database code hasn't changed hugely over the course of the game. The fundamental nature of the system is the same; dupes just take advantage of current bugs to exploit this. It is possible to have a blood clot and be bleeding elsewhere at the same time, or have multiple stab wounds, or multiple clots. Multiple groups of players working from different directions will find multiple dupes. We just need the doctors (dev team) to fix the system up a little bit more efficiently.
Capping resources won't work. If it is too low, it will frustrate other players, and scripters will just use more unpaid newbie accounts. Like with the Casca/Melissa thing, people just switched to other characters, shards, or accounts. If it is too high, it won't work either. The logical reasoning thing is also problematic. Unless you have another person at the other end, the system will be beatable eventually. I've seen programs written by unknown programmers play checkers, chess, and other games. I'm betting there is a scripter or fifty good enough to write a script to do the control tower puzzle while peacing or fighting the other swamp spawn, and that's probably one of the neater mini puzzles in game.
What are we paying for? People all have their own answers. Paying to hunt, paying to pvp, paying to keep an extra house, paying for content, paying for bug fixes. The dev has more resources than us, but they also have more responsibilities. Even if they made a new interesting monster a week, some would get bored with it in a day.
Also, we want huge epic storylines, but we expect someone else to do them. I once asked a friend what sort of event he wanted to see in game. He mentioned an epic conflict involving multiple player towns and guilds stretching over the entire world. I said "why don't we plan that?" He then basically said it couldn't be done without OSI/EA. He was wrong. Our shard has organized the Divided Lands a few years prior which was epic, big, and player-run.
I personally don't mind the mod system. I think that any "magic" item system with any flexibility, power, and utility will have a certain amount of complexity. I noticed a certain complexity to the DnD magic item system in the tabletop game for example. Maybe being a veteran of tabletop rpgs makes me better able to wade into the numbers, but I do like having flexibility. I'd hate to see some mods go away, even the ones I haven't really used.
Some way to better sort and organize items would be very helpeful.