Yeah, it's totally fine to like one Smash more than another. For example, I find Project M to be the least enjoyable version of Smash. It's mechanics are rather... Not fun. A lot of that is because of wavedashing.
To me that's like an unintentional side effect that became the staple of a mod. Let's say they make a Street Fighter game where, by setting your controls just right and doing a quick and complex hand motion, you can get Ryu to shoot a fireball and then immediately glide across the screen behind it with a grabbing hitbox. A sort of... Fireball-attached-grab. We'll call it the F.A.G., because advanced techs always use abbreviations. A F.A.G. has huge advantages against the average player, since it can't be blocked (because of the grab) and can't be countered (because the fireball's hitbox has priority). Now, some characters F.A.G. much harder than others. Some characters can't F.A.G. at all, like Honda who has no fireballs. Players stop worrying about varying play and relying on their characters' different movesets and instead focus on F.A.G.ging out completely. Players who want to win through non-F.A.G. means are at a huge disadvantage. Capcom set out to create an engaging and fun game, but instead they see nothing but F.A.G.fests, so they fix it through a patch or a new game. These elitists who have mastered being a F.A.G. user realize it's superior to everything and don't care whether it was intentional or not, so they create a mod, Project F. Project F is catered to F.A.G.s. F.A.G.s are a staple of it. The custom animations are awful, the Jpop DDR custom soundtrack is horribly out of place in the series it's based on, but this game knows its purpose, it's not meant to be fun, it's a showcase for F.A.G.s. Which would be totally fine and cool if you ever heard people say "I enjoy Project F but don't consider myself or my tastes superior to those who prefer non-Project F Street Fighter games. I also don't feel the need to tell everyone that non-Project F games suck every time I bring up Project F," but that never happens. Then again, I guess if Project F players weren't so obsessed with it being better than all other versions of Street Fighter then we might not have F.A.G.s at all. In this hypothetical Street Fighter analogy, of course.
Aside from Project M I enjoy all Smash Bros games a great deal though. Thank you for supporting my right to free speech, community. Yay for opinions!