The Federation doesn't have a basically static number of Planets. It has increasing numbers. There's a certainty of snubbing that will occur.
This is less of a concern than you might think. First off, nobody's even remotely proposing naming them after every planet; one per
major member species is the goal here- start out with the core/founding members, of which there are
four- humans, vulcans, andorians, and tellarites- and even the longshot goal of one for
every member species is quite achievable over the next sixty or so years of, y'know, almost totally replacing the entire fleet. And if one of those minor species wants theirs a little sooner, and has the economy, industry, and population base to afford it, and their people are a little extra motivated to contribute their time and effort to Starfleet? Great! They can sponsor one! Or build their own, even, we're not picky! (Andoria probably will
anyway, after all.) If not? Eh, we'll get to 'em eventually; there's no
snubbing here, just working our way through the list, and if it takes a few ship classes it takes a few classes and if not then great.
I really think it'd be a great point of
pride, for a so-called "minor member species", to see one of Starfleet's Finest with their homeworld or their first spacefarer or whoever emblazoned across the saucer, and a great way to encourage (in the gentle social encouragement sense) more interest in and contribution to Starfleet not just from their
tax revenue but from their schoolkids and grads. The Federation has benefited all of its member species, some of them enormously, and not all of them have had the population or industry or whatever to benefit the Federation in turn. And
that's fine; the Federation is
supposed to benefit its members according to their needs, not according to their pocketbook. I don't see how that contradicts the idea that inspiring them to think about if they're able to give back a little more than they have been to the rest of the Federation and the new species that might join in the future could be really cool.
tl;dr hoping to inspire a bit of species pride (specifically, pride in their species as a key contributor to and a good citizen of the Federation we all share) by honouring and expressing how much the Federation in general and Starfleet in particular
values their membership and their contribution is a long way from the sort of cynical picking-and-choosing-favorites (or worse, auctioning-off-your-name-on-the-building) scenario you seem to be imagining.
tl;dr of the tl;dr: this is the brighter and shinier future; we can have some brighter and shinier social engineering, too.