I can't deny the controls are somewhat awkward, especially in G1, but it's nothing one couldn't get used to after a while. Probably mostly complains by spastic weirdos whining about not being able to bind the mouse buttons for movement!

The two games are very good despite their flaws. But TBH, not sure I would try them now if I hadn't played them back then as their age shows. Nostalgia does play a role.
There are graphics mods, of course, and even some DX11 injector thing which improves the visuals. 

Total Annihilation was not underrated. It did not garner starcraft levels of popularity though for sure, it is also more complex/games are longer/less accessible.

M.A.X is another fantastic strategy game that never got very popular although consensus was it is a great strat game. (recently re-released on steam or GOG I think, sadly just a dosbox quickie) 

M.A.X. was ok.

Speaking off forgotten/underrated RTS games I can add 2 titles:
War Wind - very nice RTS, Warcraft meets Starcraft with good pixelart graphics;

Z - my favorite RTS. You command robots, capture zones which have factories, produce more robots/tanks and capture more areas, till you get to enemy base. No building mechanics. More area you get, shorter time it takes to create units. Sadly GOG's version is a lame port (PC => Android/iOS => PC), so better to use this open source remake engine: Zod Engine 

For anyone that does not know of this site - just in case and as it is relevant to the thread
http://www.homeoftheunderdogs.net/featured.php

Thats their best of the best underdogs but there is plenty more to discover on the website, especially the "Top Dogs"

I was most amused to discover the website is founded and run by a middle aged Thai investment banker lady :D 

I still have a TA folder, along with editing tools, and it all works fine on Windows 7.

It actually supports wide screen natively, up to 1920x1080, which is very unusual for a game released in 1997. 

http://theisozone.com 

Eh ? As to what ? A download resource sure, its not about procurement but documentation/discovery. 

Vagrant Story. Squaresoft's best game? More combat focused than their other RPGs. Lacks the party system from Final Fantasy and focuses on a single protagonist instead. Has weapon-dependant combos and damage zones on enemies. Much darker, dungeon-heavy setting compared to Final Fantasy. Almost a fantasy dungeon brawler. Pretty good story too.

Far Cry 2. Significant open-world shooter IMHO. More unique and daring, and less dumbed down than later FC games (fully diegetic interface, for one thing), also again much darker tone. Great African setting. Lots of freedom for the player. If you're bothered by respawning checkpoints, you're doing it wrong. You're not supposed to hang around the same checkpoint all day, you're supposed to be exploring. The game is actually excellent and, IMO, just as iconic as STALKER when it comes to open world RPG shooters. Much better than Crysis anyway. Didn't deserve all the flak it got.

re: Prey: I can't stand the characters and story. Some dope has to rescue his permanently screaming girlfriend from aliens. Really? Does it get any more trashy? Weapons and combat, I'd rather play Bioshock. The spirit walk and anti-grav was cool but underdeveloped. The death mechanic was yawn-inducing. 

I liked Prey, it was pretty good, and most people, Jonas aside, thought it was pretty good, no more, no less.

I forgot this one:

Satellite Reign - isometric real time cyberpunk squad tactics game. All the neon and rain-soaked streets you could ever want, and a very fitting electro soundtrack. Not hugely engaging but nicely done and stylish enough to deserve more acclaim than it got. 

far cry 2 has very good firefights.

they are boring many times, but also many other times they are the best firefights in any game that i played, and they're not scripted fights. 

I really enjoyed Final Fantasy Tactics.

Legend of Dragoon is worth hunting down too btw, not Square but still awesome. 

Myth II: Soulblighter. It's a great game in the seemingly niche genre of real-time tactics, with a dark medieval fantasy setting. Unlike in RTS games, there is no base building or resource management, you just have the units you start a level with and (if you're lucky) scripted reinforcements. Individual soldiers (which all have unique names) get buffs based on how many battles they survive and how many enemies they kill, so pyrrhic victories are discouraged. It can be potentially very difficult for this reason, especially since the game does a pretty good job of making you actually feel like the commander of a dwindling medieval army desperately fighting back the hordes of undead. Picking your battles is important, and the levels where you have to hold your ground in the face of a horde are always brutal. The game has a cool physics engine for the time, rendering every projectile as an individual physics object, even subjecting them to weather effects, meaning making effective troop formations and taking advantage of terrain are really important.

Another one is King of Dragon Pass, a sort of hybrid RPG/government sim based in the stone-age high fantasy Glorantha setting. The setting's lore is integrated into the mechanics of the game in some pretty cool ways that aren't immediately obvious.

Finally, this may not be "underrated" so much as a cult thing, but Yume Nikki is the holy grail of weird-ass arty indie games as far as I'm concerned. 

Myth TFL was great and Myth 2 was good too; they were almost as big as Quake was for me in 90's gaming shenanigans.

Fingers crossed that http://store.steampowered.com/app/346930/ has some of that same gameplay flavor; it's pretty rare. 

Well Myth TFL & Myth 2 were my favorite games when I was a child, never get into multiplayer, I tried it recently but it is super hard to learn.. and I don't believe everyone has that much patiency.

Third one, Genesis Ghostbusters. Only genesis game I have beat too many times, something about it just feels right to me.