This one too, 90s must have be the golden age of rts. Total annhiliation remains to this day my favorite rts ever, though supreme commander comes really close (pretty much a sequel anyway).
I feel like a lot of developers saw the increased capability of newer hardware in the early 2000s, and decided that meant the time had come to add
more stuff. Wider varieties of units. Larger numbers of units. Larger scope of the game. Flashier, more eye-grabbing graphics. Fancy, processor-intensive game mechanics that made the combat more like a realistic simulation and less like a straightforward application of easy-to-understand rules.
All of that made for games that sounded impressive. In fact, they actually
were impressive... for the first few minutes playing them.
After you'd played for an hour or two, the "innovations" stopped being impressive and started being frustrating - controlling 1000 units is actually not more fun than controlling 100 units; either way you're just personally managing a half-dozen groups, and a higher number just increases the odds of having straggler units lost or overlooked, plus shrinking the size of unit models and making mis-identification errors more likely. Having 20 different types of soldier in your army is impossible to micro as effectively as just 3-5 types. Smoke, fog, shadow, non-transparent 3D models, debris flying around, and other graphical features that look good may also interfere with the ability to size up the situation at a glance, which breaks the flow of the game.
Changes to game mechanics to enhance the detail in which combat is simulated can enhance the "realism" of combat simulations and make for more immersion, but it also can make it harder to understand and intuitively predict how the set of combat rules will impact any given situation - and thus make it harder to come up with innovative strategies on the fly.
Late-90s games, through a relentless focus on refining the things hardware at the time
could do, managed simplicity perfected. Early-2000s games managed complexity half-a**ed. And it absolutely killed the genre - a whole generation of players learned that RTS games were confusing morasses that sucked you in and left you scratching your head wondering what just happened. I'm... just a touch bitter about this.