I was thinking of getting these two stats maxed because I liked the idea of making badass armor for myself, but I'm worried that it'll be TOO badass and break the game difficulty. What I'm wondering though, is if I don't abuse any of the "fortify loops" I've been hearing about, but I still max both trees and make powerful enchanted armors and weapons, will I still be too over-powered? Do I have to go out of my way to make things too overpowered, or will I inevitably be an invincible killing machine, even on Master difficulty, just by enchanting?

I've maxed my crafting skills, and I've taken advantage of the loops, but I still haven't broken my game. The reason is mostly that my self-control kicked in when it came time to choose my enchantments. I resisted fortifying my combat skills, instead choosing things like waterbreathing, increase carry weight, etc. My enjoyment of the game was actually increased, because I like the process of crafting, creating potions and (especially) poisons, and enchanting, but also because having the excellent equipment freed me up to choose non-combat perks, like pickpocketing, speech, etc, rather than maxing out the damage- and armor rating- increasing perks.

Armor rating isn't really an issue, since there's a damage reduction cap (iirc, 80% reduction, reached at 567 displayed armor rating, with 4 pieces of armor equipped), but if you smith your weapons endlessly, enchant your armor with fortify combat skills enchantments, etc, you can break your game (unless you enjoy smashing through enemies, which is fair enough). You can break your game that way without taking advantage of the loops; and you can take advantage of the loops without breaking your game that way.

With those two skills you can really overpower your armor and weapon: Boost your enchanting with potion and make amulet, gauntlets, armor/clothing and ring with fortify smithing ability. Then wear them all and also boost your smithing with potion too and then upgrade your armor and weapons.

I wasn't going to do that though, just enchant without any "fortify smithing" boosts.

I think as long as you aren't going out of your way to grind/power level your Enchantment by spending a ton of time just making Ring of +1 Magicka, your skill should advance at a rate that keeps up with the game's difficulty curve. The issue comes when you spend a disproportionate amount of time getting über-enchanted really early, shooting zero-cost Incinerates constantly, I think.

In short, yes. The biggest culprit is the fortify damage enchantment, which at fully perked 100 level enchanting will give you almost a 40% damage increase times four enchantable items, without using a fortify enchantment potion, let alone looping them. Just to put things in perspective, your weapon skill can be perked up to +100% damage, with an added +40% damage from getting to 100 weapon skill. That means fully leveled and perked enchanting can increase your damage more than your chosen weapon skill can, with every skill in the game simultaneosly (excluding destruction), just from one single skill tree that, unlike combat skills, can be easily power leveled.