You can’t just “spam as much as you want,” since you’re limited both by available resources, the availability of creature dwellings, and the production limits of creature dwellings.
Upkeep’s a valuable concept, but you have to understand why some games have upkeep rather than just assume it should apply willy-nilly to every game. The primary purpose of upkeep is to put a curb on expansion rate. A lot of 4X games have a potentially exponential expansion rate - the larger your army, the faster you conquer production sources, the faster your army grows. Upkeep retards that by increasing costs as your army size increases. That’s not a particular problem with the HOMM series since there are a number of other curbs on growth.
By “bazillion resources” I assume you mean the variety of resource types. While I agree it’s a bit excessive, you don’t understand the game if you think they don’t exist for a reason. You can group them in tiers, with wood and ore at the bottom and crystal and gems at the top. High level creatures require the upper tiers. Both for the creature dwellings and to purchase the creatures. An intelligent map design will often restrict access to upper level level creatures by restricting production of upper level resources. Further, some resources are tied to some factions, which can restrict what you can build.
This is important, because one of the serious problems with Heroes II was that the highest difficulty level gave a flat per-week production bonus to AI players. This broke a number of maps, because those maps were balanced around the difficulty of obtaining resources like gems. One of the significant improvements from II to III was that III used a multiplier for production bonuses, rather than a flat addition. If the AI had no gem mines, it didn’t get additional gems at any difficulty.
A number of your other comments, such as stacking being “wonky,” are just a way of stating that you like one game better than the other, rather than actual points.
I wouldn’t say the Heroes series is particularly deep. Certainly it was never as complex as Civilization. There are a number of significant flaws, such as the number of near-useless skills and spells, such as the infamous Eagle Eye. It suffers from a certain seat-of-the-pants, kitchen sink design, which I understood better after working with JVC. Jon didn’t really grok numbers or balance, and tended to just throw stuff that looked good into a game. For the most part, though, this worked out pretty well with Heroes.
I personally never much cared for the original Age of Wonders, which I first encountered when I was working at Interplay, at least a year before I moved on to New World and got to work on the Heroes series. I can’t give you a detailed analysis now, because unlike contemporary games like Civ I and Heroes II, I only spent dozen hours or so with it before deleting it. It may have been expectations, since it tried to present itself as a Civ-type game rather than a Heroes-type game, and it suffered badly in that comparison.