It is not so bad as it was in Oblivion as I've see Drauger (spelling?) that have gotten steadily easier for me to kill. I've seen the scaling primarily on bandits and certain wild animals.
No, I'm understanding you perfectly, but you seem to not grasp the fact that you won't be any stronger in combat because you spent your time leveling up your skill in alchemy while neglecting your combat abilities.
I'll put it this way with the age-old stereotype: The nerd gets pounded on because he's smart with books, but weak compared to the jock. If the nerd spent a little more time on getting physically stronger instead of only just mentally stronger, he'd become more able to stand up for himself physically against the same jock.
This isn't some traditional JRPG where leveling up means arbitrary increases in everything, this is different. In this, you level up according to the skills you use, so that the more you focus on stealth, the better you become at sneaking around and either getting sneak attack crits or otherwise bypassing threats to get the loot. If you spend all your time on getting better at making potions but none at all on improving anything related to combat, you will have a harder time at combat as you rise in levels compared to everything else. Kind of like if you don't hit the gym once in a while, you're going to get soft and fat, instead of lean and trim.
I honestly feel like I'm being Captain Obvious here, you really don't understand that???
The levels are typically locked to your relative level in dungeons at the time when you first enter them, and they don't scale as much, while other areas will own you if you're not powerful enough. The idea of the scaling is that you still get something of a challenge from time to time, especially when you get into the upper levels, because by then you will have plenty of higher leveled skills and upper-tier perks and gear to utilize.