First of all, thank you, Gents (in the non-specific gender usage), for your work on this game--may history praise your efforts! Perhaps 20 years from now, a game designer will call their game "the spiritual successor of Fallen Enchantress."
(1) We know how critical people can be of a game with potential that falls short (I keenly remember the disappointment), so the more you can keep Elemental: WOM in the past, the better (except the hard-learned lessons, of course). A name is so simple, yet carries so much weight/prejudice.
(2) My compliments--such a nice looking site. Makes me really want to play that game.
(3) Many of Sean's suggestion have merit. In the most general of terms, there should exist a wider range of useful spells (even if for certain situations only--as long as they are well explained and seem cost-effective, then they will be a wonderful addition). And hey, Brad, how fun will it be to update certain AI opponents to intelligently use some of them (even to the level of signature tricks that must be understood and countered)?
(4) Surely more quests can be added over time to reinforce the sandbox nature of the game--I love playing the game for the 10th time and seeing content I've not seen before. More wildland areas that are treated like major quests cannot be a bad thing, either, where the random generator can pick a certain amount of non-required areas per map size from a long list, further adding to the unique feel of a particular play-through (tricky balancing, but would pay huge dividends).
Caveat: All quests must be properly explained, and the fun surprises be carefully balanced as not to wipe out a player's game. You want a challenge without resorting to blindsiding the gamer--let them know in no uncertain terms the can of giant worms they are about to open (and please kill that design flaw where if they want to come back to a quest later they cannot because it's gone). Think of it like storytelling, where the best suspense, the best action, is seen coming like an inevitable tidal wave (or at least cleverly alluded to, in the mildest form of foreshadowing).
In general, I believe an increasing feeling of epic with each quest difficulty level is a guiding ideal, with the later difficulties including mechanics like multiple waves of enemies (properly introduced, not just thrown in like an afterthought), more meaningful choices (like the defend/attack a certain faction) that perhaps even reverberate within the game at large (a large ripple might cause a severe reputation drop from someone, even inciting a war--that kind of tying in, if balanced, is a great example of that epic feel). Ever considered a quest choice can trigger one of your "random" events? A wealth of possibilities.
(5) See above quest section. I feel most random events are poor substitutes to triggered events based on questing/actions. Randomness often triggers that unfair/blindside mentality that so many people despise. Consider this: you can add much semi-randomness without that feeling if the gamer knows that "because you did <this> then <this> begins to happen." The random application of triggers would scratch this particular itch. For instance, going on a clear killing rampage (razing more than 2 cities, perhaps) might in one play-through do nothing, yet in another it triggers the wrath of an old god who counters the move by sending his minions against the offender's capital city--you can start this triggered event well away from the city, with a portent as a clear warning (essential to a good design, IMO, so as to avoid the nasty blindside).
Another example off the top of my head: when completing the first building required for the Spell of Making, a lingering elemental force (like a pocket of trapped gas) sometimes explodes, and unruly elementals (perhaps antagonized by the shift in power) attempt to destroy the cause (would target the city that building is constructed in).
Even a purely random trigger (like the blood moon that triggers a monster increase in wildlands areas) can be properly noted a warned-against (heh, we've been building plenty of cleric housing and such, so make those chumps useful).
(6) It would be dreamy if you could have several different strategies (with different strengths/weaknesses) for each major AI house. This way players aren't always sure what they're going to get with a particular opponent--perhaps a % chance one opponent might "borrow" strategy from another opponent, just as you would borrow strategy from the cleverest of beta testers (which does not include me, since my success is largely from taking advantage of the weaker opponents to make my steamrolling inevitable, heh, though this in itself could be an interesting strat--for one AI to "exploit" another to gain an edge). For example, one game, the Master Scout races will take advantage of their trait to over-expand (leaving them far more vulnerable to early military action, which would perhaps make them change their tactics to turtle in their first 3+ cities before regrouping and lashing out again); another time, this same race could use their trait to quickly grab resources, and then spend their efforts protecting/growing those resources until war is declared on them. Sometimes a tactic might include aggressive actions, and sometimes more cautious actions, like only going to war when using an alliance.
(8) I contend good modding should be difficult to do correctly only because the core game is so beefy and polished. The whole modding-as-bug-fixes done in so many games these days leaves a sour taste in my mouth.
(12) While my time is limited, if you need another leak-proof editor to give fresh perspectives, count on me (though I imagine Dave comes with his own resources).
Label me as a fan with balanced expectations.
*I'm guessing many testers will dislike my suggestion of a more extensive and flexible tech tree, but allow me to make one last case for it. When techs become too concise, they seem linear--currently, it's simple to follow the path of least resistance (lowest cost tech) and get everything you need for a fairly optimized victory. More options that seem somewhat exclusive of each other lend a flexibility that isn't obtained in any other way. You can play different leaders with different traits on different maps, yet you tend to follow the same tech path. This is like leaving potential on the table, IMO. In general, players should be able to dive "into" a certain line of research at the cost of other things. The less repeatable your tech path has to be, the better (so long as there is no fluff/worthless techs simple to bump up the count).
*I strongly feel each possible ending should be more epic, more sweet, giving a level of satisfaction that makes the gamer sit back, savor, and almost be sad it's over (solved, of course, by beginning anew). 4x games have traditionally spent next-to-nothing on the endings, but I ask you this: if the length (time investment) of a game is so huge, shouldn't the ending match to prevent the anti-climatic feeling? An otherwise great novel with a hurried/cheap/unemotional ending can ruin the entire experience. Rather than make a dig against Fallen Enchantress, I want to define why it's so important to elevate the gaming experience upon finishing the game. Some might claim the ending isn't important, but would they really dislike or ignore a powerful conclusion to their experience? I cannot image that being true.