The more you play and further you get, guys adopt new equipment that can be annoying. If you're used to sniping tranq shots from far away, soon everyone will have a helmet. Shoot them in the face, and they get a visor. Later on most squads have one or two guys in riot gear as well on patrol, so you can't tranq them period. Makes you use your CQC and hold up, which I find a lot more rewarding anyway. Also, areas that were sparsely patrolled before might now have a gunship there or armored vehicle units.
So yes, it becomes more challenging, but never insurmountably so imo. You'll get mission variations later on, like a main mission you've already done but a new stipulation like: No reflex, no hats, OSP (onsite procurement) of weps only, and everything has better visibility (like a hard mode) - those are called Subsistence. Or extreme missions where everything does a lot more damage (those are usually skull missions). Finally, you have total stealth, and the name implies the parameters.
Early skulls are easy, just use a LMG and dive away from giant exploding pillars they make. Later on (way later on) when they're 'extreme', use a brennan sniper rifle because it has the most piercing.
There's 50 main and 150 side ops I believe, so you still have a lot to go and time for the difficulty to increase.
If you find the game too easy still, I'd suggest going non-lethal (which I would always suggest because it's more rewarding). If you're already doing that, trying turning off reflex mode in options, because it keeps you much more honest in your infiltration.
The few times I found something 'frustratingly' difficult was usually just because I was going about it the wrong way. When I see people say something insane like, "My finish time was 97 minutes", my eyes bulge and I wonder what the fuck you were doing the whole time. If something seems 'too hard', you're probably just not thinking outside the box and need to take a small step back to reevaluate.