I never considered that as an advantage, so you'll have to be careful with inner plugin dependency, which is not documented at all but used heavily. However I think the source is clear enough to just do it.
Also, at 2.5kb when gzipped, I normally just put the whole thing (:
I think it'd be really complex to include the whole @requires tree manually since it's actually quite long (for instance, toggleClass depends on addClass() which depends on eacharg(), which depends on args(), which depends on each()).
Maybe splitting it into a "core" and "plugins" would be a better idea but then we'd also need to separate the plugins by type, as .adjacent() is used by .after(), .before(), .append() and .prepend() but by nothing else so it's not really a core plugin but also a dependency. This also has its problems.
So I think in total is not really worth it.