Well, it's not SMF being like that, it's the sites that insist on proper XHTML... which can have SEO issues (and will be just as much of an issue in ANY system)
Of course most mods work on the default theme... they were designed for the default SMF theme, and yes, if a custom theme does something custom it's going to be a problem... this is expected. It's part of the design, to a point.
SMF 2.0 just doesn't offer the functionality to support doing it with hooks, 2.1 isn't a lot better, Elkarte and Wedge are much stronger (especially Wedge) in that department.
2.1's theme, Curve II, isn't actually that nice. I find it quite bland, actually.
Of course most mods work on the default theme... they were designed for the default SMF theme, and yes, if a custom theme does something custom it's going to be a problem... this is expected. It's part of the design, to a point.
SMF 2.0 just doesn't offer the functionality to support doing it with hooks, 2.1 isn't a lot better, Elkarte and Wedge are much stronger (especially Wedge) in that department.
2.1's theme, Curve II, isn't actually that nice. I find it quite bland, actually.