Q: Why don't people like SkyRE on /tesg/? Why do they insult me for suggesting it?
A: The #1 cause of dislike with SkyRE are compatibility issues, though a close second is a general aversion to modding laziness. Large overarching overhauls to the game can add a lot without requiring a large amount of customization or installing a lot of mods, but when you do that you're playing what someone else felt the game should be, and many of us strongly dislike that. Customizing a game to your specific tastes isn't always fast and easy like installing a mod overhaul.
Typically it can involve downloading dozens of mods, installing them, configuring them, adjusting them, and in many cases deleting them and restarting your characters. It can take dozens of hours but the end result can be a Skyrim experience that is completely unique to you and what YOU find fun and enjoyable. Mod incompatibility is one of the biggest challenges to creating a Skyrim experience and that's where a great many overhaul mods fail. The more you change, adjust, alter, and modify with your mods the greater the chances are that other mods will be broken. SkyRE adjusts quite a lot which makes a great many other mods run into conflicts and incompatibilities.
While many of those mod authors produce 'compatibility' patches others may not, and you can easily run into a large amount of issues when those mods do come into conflict. The third point in the reason why we don't like SkyRE is because everything it does, we find better alternatives for. This point is largely one of opinion and many will disagree with us on this, but to give one large example - the perk overhaul most widely recommended is Skyrim Perk Enhancements and Rebalanced Gameplay (SPERG). SPERG is, as you would imagine, completely incompatible with SkyRE but since it adjusts far less it has far fewer conflicts with other mods. It's also more customizable, but this isn't a question about why to use SPERG so we won't go into larger details.
Suffice to say that anything that people say that SkyRE does, we find other things that do just as well if not better AND typically have fewer compatibility issues. The last point is not so much a criticism of the mod itself but of the mod author. T3ndo is notoriously bad at taking criticism for his mod and we generally find his work suffers as a result. His little comics that he draws for his mods are creepy too, but that's another story.