In X-Com, prohibit saving and reloading in the missions (or do an ironman approach that quit the game whenever you saved) but also dramatically decrease the number of permanent deaths, and instead incapacitate your soldiers. Also, make the number of soldiers that you can take into a battle much less (maybe halve or 1/3 them), and empower them by introducing a specialization/skill tree system or somesuch to make the RPG elements actually able to be understood by the player. Do a point-buy character creation for each soldier instead of just rolling for their stats. Clarify what the stats do, and also introduce some mechanic to detect general locations of aliens so that you're not left traipsing around looking for that last alien in the map for 1/2 to a third of each mission.
As it stands, it's incredibly easy to permanently lose your soldiers from a single random shot from somebody you couldn't see. I still haven't finished the game because it became too tedious to do the same reload/save spiral to figure out alien locations and to prevent your soldiers from dying, and slowly move 12 soldiers across the map to look for that last guy on every single mission again and again.
In Planescape: Torment, tweak and balance the combat to give a much more robust Baldur's Gate feel to it. It's basically mediocre; even though it's not the focus of the game it is still a very prominent part. I'd be more specific, but it's really just a matter of adding more characters, more options to allow those characters to pick, and making sure that those options are each viable but not too powerful.
In Persona 3/4, making the skills that a persona is fused into have be selected from a menu instead of randomly generated. Spending hours to find the combination of skills you want is the single worst part of those games.
Final Fantasy Tactics - changing experience to be awarded equally to all characters in a battle instead of per action. I'd grant access to several basic skills in your current job if you haven't already earned them to not force players to rely on skills from a second job to make their cleric get experience/JP. I'd rebalance the broken abilities, too, such as forcing the Calculator's Math skill to take the same amount of time to cast as casting the spell once normally in addition to costing MP equal to the amount of times the Math skill ends up landing the spell. Change Blade Grasp to work (Bravery/2)% of the time to prevent it from being near-invincibility. Remove the ability on Teleport to teleport further than your normal speed with a % fail chance. Also, make the Move-Find item always give the better item regardless of bravery.