Space Empires V. Brain the size of a galaxy, can't do basic math. You can literally reach arbitrarily high values in formulas when modding this game by adding and subtracting 1 to itself in alternation, simply by abusing the script engine's broken order of operations. Something along the lines of, 1 + 1 - 1 + 1 - 1 + 1 - 1 equals 5 or something. I have no idea how that even *works*...
Also, you want a replay of your simulated battles from last turn? Well, guess what? It's 50 megabytes! Because instead of storing "Ship A fired bullet at ship B at T=5 seconds; bullet struck ship B at T=6 seconds and did 20 damage", and interpolating the bullet's position in the second in between client-side... the game stores "Ship A fired bullet at ship B at T=5 seconds. Bullet moved a millimeter across the screen at T=5.05 seconds. Bullet moved another millimeter at T=5.1 seconds..." ad infinitum.
It would probably be more efficient to store the battles as HD videos; you'd only lose the ability to pan and zoom the map!
Mega Man 5. Not my favorite Mega Man game, but I love the series in general, so I think it counts. Mega buster is WAY overpowered compared to the master weapons. If you're looking for a game to do a buster-only run, this is it! Unlike in 4, the charged buster shot is as tall as Mega Man, and on top of that it does something like 5 damage, as compared to the 3 damage from Mega Man 4. And if that wasn't enough, Mega Man 5 has the most useless master weapons of any Mega Man game in existence. Only three of them (the Gyro Attack, Crystal Eye, and Gravity Hold) are actually practical enough to bother using; the rest are so impractical to aim (especially the Power Stone) that it's actually harder to defeat bosses weak to them using the appropriate weapon than using the mega buster! (But hey, at least there's no Top Spin...
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Metroid. As stated earlier in this thread, grinding for health for what feels like 15 minutes, only to lose it all to a boss in 30 seconds, is not my idea of fun. This would have been a far better game had you started with full health after you die like in most of the sequels, or if there had been health refill stations scattered around like in Super Metroid.
Master of Orion II. So you have a battle with hundreds of doom stars vs. an enemy fleet with dozens of battleships and titans. You're sure you'll wipe the floor with the enemy, but it's going to take a while. What can you do? Not much. There's no "skip battle" option; the best you have is a fast-forward autoresolve which can still take some time on battles of this size. Guess you might as well grab a cup of coffee... at least they added the autoresolve in a patch!