Overall MGS game quality? That seems to be a hugely subjective thing.
I personally like Peace Walker a lot. The controls felt surprisingly smooth and modern considering the PSP's restrictions. It of course feels superb on the Dual Shock 3. I already explained why the base building works so well -- I felt a real feedback loop out of it. The missions, while small, I think still display really good level design. Visually I also like PW's lighting and color palette. The only thing PW fucked up in my opinion are its boss battles, which were obviously balanced around co-op.
I don't think I can really offer full opinions on MGS1 and MGS2 because I haven't been analyzing them for 10 or 15 years like everyone else -- I played them for more or less the first time around 2007 or 2008. I personally still don't like how much MGS2 makes you go without the codec. It really shows how old fashioned its reliance on fixed camera angles is. In that way it has the same problem as classic Resident Evil. In MGS1 that style of gameplay works in tandem with the codec because MGS1 is basically a top-down 2D game. I look back on MGS2 as a half-step into 3D for the franchise.
That step wasn't really complete until MGS3 and the third person camera in Subsistence. Taking away the codec but giving you the tools to actually explore your environment brought MGS3 closer to being a traditional 3D stealth game like Splinter Cell or Thief. From there MGS3 amazes and continues to hold up today due to exceptional encounter design giving rise to memorable moments like the battle with The End. It also does a great job of setting up all those encounters in tandem with its themes and the transitions of its plot. This offers a great sense of movement from place to place as if you're on a journey with Snake.
My idea Metal Gear game would probably be MGS3 with a more modern control system (like in the 3DS version but with two sticks).
MGS4 I feel actually has really great core gameplay systems, but doesn't give you enough opportunities to actually engage them. After the first two chapters the game flips on its head with a bunch of alternate gameplay segments that just ended up being underdeveloped ideas. You get a nostalgia trip for MGS1 fans, some admittedly great boss battles, a short chance to re-engage with the actual core gameplay systems at the beginning of chapter 5, and then cut scenes that go absolutely insane from there to the ending.
I guess I get it if you're not feeling the base management since that's not what you normally do in a Metal Gear game, but the big change I do like is its emphasis on much more open-ended missions. The kind of mission design you see in Ground Zeroes I feel is when a stealth game is at its best. It reminds me the most of Chaos Theory and Thief. Maybe if they did make a more traditional Metal Gear game that was just a linear chain of Ground Zeroes-like environments it would be the compromise some people want. That would come off as a more advanced version of MGS3 I guess, and I feel like that's basically what Crysis 1 is.
But what we have here is that ideal blown up into an open world that you just infiltrate. I think this is what Kojima imagined when he thought up the idea of sneaking into Outer Heaven way back on the MSX in 1987. He just didn't have the technology to design it into a whole "country" like open world games do now. The end result to me looks like what Far Cry 2 was trying to be, but more developed.
MGS2 probably has the most varied main mission, but I don't see why you couldn't have variations of all of those themes in TPP.
Find this guy using an audio cue, find a way into here, help this person, etc. There could be hidden alternative ways to complete some missions but that's no bad thing.
I guess you can replace number 6 with the crazy sounding prologue mission.
If we're gonna talk about mission variety I have to take this as another opportunity to mention
Metal Gear 2: Solid Snake. I really do consider it to be one of the better Metal Gear games overall. It's basically MGS1 eight years before MGS1 with slightly more varied gameplay.