It is not as goofball as some like to claim. Just very broad in its tone from deadly serious to very lighthearted.
Yeah, I don't mind lighthearted, but I think Spelljammer didn't have as solid a tone as other campaign settings. Joke races and biomechanical elves. (It sounds cool, but the writeup was pretty dull)
I think if I ran Spelljammer nowadays, I'd focus on a Jules Verne / Adventure Planet type of tone, and not be distracted by the grab-bag of ideas floating around.
My first response to Spelljammer was I wanted to rewrite the whole thing. It's cool in conception, and when it comes to a lot of the specifics, but there are the usual mechanical issues that beset everything in second edition, and as you noted, it's very inconsistent in tone. It's a place with a lot of wild ideas, but some fail, and it generally feels like it's more in the brainstorming stage than a final, polished product.
I think this was more of a problem when it first came out, because the main audience of D&D at the time was teenagers, and people at that developmental stage are great at absorbing vast gobs of material, but they're weaker on the critical side. Most gamers today are experienced adults, with a broader perspective and firmer ideas on what works and what doesn't. Spelljammer works fine from that perspective. It's a grab-bag of ideas, but it needs a filter. Decide what works, drop anything that doesn't, decide what to focus on, and adjust as needed.