Well the thing with Mega Man X is at the time it wasn't made to be a spin-off series, but a sequel/reboot. Or the new direction of the series at least. Things just went weird when Mega Man 7 came in and started muddling with the timeline. Video games are confusing.
It was definitely Master of Shadows since SoD is from this year. And improves on it in basically every way. Another game that would fit your most improved sequel list.
See, that's why I usually recommend people start with 2. They repeat the twist so in 2 it felt fresh to me when I played it for the first time and there's nothing from the original you need to know both story and gameplay wise. Either way though, it's an incredible game and one of my favorites. As for your question:
Pokemon Gold/Silver, Ratchet and Clank: Going Commando, Crash 2, Super Mario Bros 3, Super Castlevania 4, Mega Man X, Assassin's Creed 2, Zelda: ALttP, Super Metroid, DKC2, Final Fantasy 4, Phatasy Star 4, Street Fighter 2, Soul Calibur, Sonic 2, Tomb Raider Legend, and Smash Bros Melee off the top of my head.
Try Styx Shards of Darkness. It's probably the best take on this kind of platforming even if it's not really like old school TR or PoP, but the platforming is still much more intense in how it works with the stealth. It also happens to be the closest thing out there to a new Thief game.
There's fewer and fewer gunfights as the series goes on. 2 still has quite a few, but balances them better with the other elements. Once you get to the PS4 games, you spend under 1/3 of the game in combat.
I think giving it a combat focus was the right call for Samus Returns. It has a structure that supports more combat since it's centered around boss fights. I wouldn't say it's the right one for any other Metroid, Prime 3's heavier combat took away from its best parts while Other M's heavy combat ruined the series. But since it's based on finding Metroids (ie exploration) before the fights, it works here. Here's hoping Prime 4 is mostly like Prime 1/Super though.
I wish I could help with your game, but my art and music skills suck. I haven't played AM2R, but Samus Returns is a damn fine game where I stand. Top 5 this year so far for me, which is saying a lot with how great this year's been (and there's still more on the way). Jak is also always awesome. Might be my favorite collectathon platformer depending on whether you'd classify Sly 2 and 4 as them.
Yeah, the shooting in Uncharted 1 gets very tedious. That's why I usually advise people to jump straight into 2, balances the gameplay elements better and any story tidbits worth mentioning are recapped well really naturally.
I'm glad Destiny 2 PC is coming out later. It'll let me know exactly how people who were lukewarm on 1 will think of it so I know what to expect going in.
