Which version are you playing, out of curiosity?
The HD collection.
I'm getting a little frustrated. The game has spent absurdly long on tutorials and story introduction but I don't feel quite like I learned how to play. Right when I felt like I was beginning to grasp the stealth the game locked me in a fairly cramped/linear space with 8 elite versions of the normal mooks and told me I had to defeat all of them. I guess repeatedly hiding under a building is one definition of tactical espionage action. The controls are also pissing me off. The crouch/prone/roll controls bind entirely too much to one button and one stick. The act of readying and aiming a gun is needlessly involved and worse, once you start aiming you can't necessarily stop without firing the gun (can't hit RT if you're in a place you can lean, can't stand up or crouch if you're prone in a crawlspace). This seems kind of egregious in a stealth game.
I knew what I was in for when I went back to play an old game so that's fair, but god there are some odd decisions with the controls. In some cases the control binds are needlessly efficient (there's no door opening button, you just walk into it) in some cases they're needlessly wasteful (there are two context sensitive keys).
Edit: Beat it by switching back to the original camera angle rather than the third person one. Still didn't perfectly work; the area is divided by walls but still open enough that an enemy on the roof can spot you without you yourself seeing him. Also forgot all that headshot and stealth bullshit and did it with good old run and gun silliness.
That's just how this series plays. It's got awkward controls even all the way up to the very new MGS5. But they're rooted in 3 decades of history and thus if you've stuck with the series for most of it's lifespan, you're used to it.
Despite all that it has improved immensely. Without even going back to the 8 bit era, Metal Gear Solid 1 didn't even have the ability to aim weapons nor did it have analog stick support. You used dpad controls to vaguely sort of point Snake in the direction of the enemy and shoot at them hoping you hit.
I'll be honest, I love the series, I love everything about it. But the gameplay can be infuriating sometimes. Before TPP came out I did a run through of every canon game I could get my hands on. (Didn't have a PSP so those stayed out of reach other than Peacewalker on the PS3). I started from the beginning with Metal Gear 1 and 2 and worked my way through the series in release order. Excepting a noticeable downstep in gameplay that was made in Peacewalker in order to fit it on the PSP with it's hardware and controls, it has improved immensely with every iteration. However, 3 was probably the peak of improvement before you reached diminishing returns. You can go play 4 or 5 and come back to 3 and not really have much of an issue with "old game syndrome" because despite the improvements later on, 3 sort of cemented the basic form of the series from that point on.
(Some would argue Solid 2 was a bigger step up from Solid 1, and I can respect that argument, but 2 was still very experimental. New things were being thrown in and the full extent of the hardware was still being tested. Mistakes were made, but it was still a good product. 3 however was the final masterpiece of the PS2 era. Everything had been tested and polished to perfection. What you got with 3 was the best Metal Gear they could provide at the time, and it still holds up because of that. And in many ways it's still my absolute favorite of the series.)
Not that anyone asked my opinion.
tl;dr: It's metal gear. Expect plenty of built in awkwardness.