When you reach the "max level" of 50, will skills continure to raise? Is the only difference that you just wont gain new perk points?

50 is simply a soft cap, meaning you'll level much more slowly. You'll still get perk points, and you'll still level. You'll reach maximum level when all your skills reach 100 points at level 81. This also means that you only have 80 perk points to distribute out of 250 possible perks, so choose wisely.

You know, I really don't like how you have to essentially fully invest perks into the smithing, enchanting, and alchemy tree's in order to make really amazing gear..

I mean on paper it makes perfect sense.. But it takes so many perks to get there that it really hurts your character.. Even at level 81. IMO it would have been beneficial for the player to get a 2-4 free perk points for each of those tree's through NPC training or something.. Idk.. I just don't like how I have to sacrifice my characters abilities to craft better equipment.

P.S. I realize that having uber-upgraded gear is a benefit in itself.

That's just another example of balancing. You're not meant to absolutely excel at everything. Pick a given combat style, use your perks to boost that. For example, I'm making a sneaky backstabber. 13 perks to max out Sneak, 8 to max my damage with swords (or just go with 5, if daggers don't count as swords, I'm not sure on that). Even if I invest in power attacks and dual wield as well, that's 15, tops. Maybe get the 10 perks in light armor to help me survive once they notice I'm there. 38 out of 80 perks used so far, and I've just capped out my capabilities for my offense/defense style. 10 perks to max out smithing, 13 to max out enchanting, 15 to max out alchemy. So, another 38 perks used, for 76 out of 80.

Perks are there to have you be the best at something (Except smithing, it doesn't look like you can do much with it without perks). It's not a requirement to use it. I may use block, or restoration, or conjuration to help myself out in a pinch, but it's secondary. My example above also assumes I'm taking every perk related to the skills in question (outside of one-handed, it's assumed if I'm dual-wielding blades I won't need perks for maces or axes). I really don't need all three tiers of Experimenter, and could probably live without snakeblood or purity. Probably don't need Green Thumb either, unless I'm being very frugal. As far as enchanting goes, could probably go without frost or storm enchanter if I just use fire damage, and soul squeezer and soul siphon aren't needed to make the best gear, they just mean I need less soul gems for recharging. Could remove the four power attack perks from one-handed if I don't use them, not sure how effective power attacks are in this game (I know they were generally unused in Oblivion). If I'm frugal enough with my perks, I could even open up a 7th skill to use at its best.

Anyway, that's just my thought on things.