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When I played Heroes 3 for the first time, I wasn't familiar with Heroes 4, 5, or 2, and I was happy with it. Later, as I progressed through the expansions, some dissatisfaction began to creep in... although not strong enough to make me abandon Heroes 3 forever. I'll list everything in order:
1). The inconsistencies of the expansions are incredibly annoying. Many creatures, buildings, and objects on the adventure map simply don't fit the original style of the game. Starting with Armageddon's Blade, the maps began to resemble gypsy camps. A bunch of gaudy, disharmonious structures, haphazardly placed next to each other, with no regard for the terrain or style. Some characters look like they've come from a completely different computer game. That's why I mostly play "The Restoration of Erathia" and "Chronicles of the Heroes."
2). The music. At first, it's enjoyable, but after about a year of playing, it starts to become incredibly irritating. I either turn off the music completely in Heroes 3, or I remove the original files from the corresponding folder and replace them with something else (sometimes I create very interesting playlists!).
3). Regarding combat: I'm annoyed by the invulnerable heroes who passively stand on the battlefield, not moving a muscle. Casting various spells looks exactly the same on the hero, after which he continues to stare blankly at the battlefield.
The meager amount of mana is also incredibly frustrating. Of course, an Expert in Intelligence with 10-20 points of Knowledge doesn't have this problem, but you have to level up to that point... and what's the point of giving magic at lower levels if it can only be used "on special occasions"? Wells, mage guilds, and mysticism don't really improve the situation; it's still awful.
4). The 2D battlefield. When you have nothing to compare it to, it's perfectly acceptable, but for a dedicated player of Heroes 4 (which I am), the flat, cardboard-like creatures don't even seem funny. However, there is one advantage to the two-dimensional battlefield: it's easier to calculate the turn-based movement and protect the ranged units.
5). The hero upgrade system. Skills are not chosen; skills are given from who knows where. Probably, they flow from another universe into the sinful head of our hero. When you're offered a "wonderful choice" between Scouting and Literacy, and you need at least some *magic*, you want to load a save from nearby. However, in Heroes 5, the skill system is practically the same, and in Heroes 4, you have to go to a special reference book and see what your hero's subclass can possibly get, and what it can't. IMO, this is a flaw of the entire Heroes series.
...but overall, Heroes 3 has far more advantages than disadvantages. But we'll talk about them in another topic and at another time.