This is basically not fixable without moving the problem somewhere else. It's messy because there are so many distinct collision rules, but try going through and computing how many gismu can technically exist at the same time. It's not as big a number as you'd think. Without getting into the various rules introduced later in the CLL (which were meant to reduce problems like these), the number is still only around 22,000. Here's a way to get started:
5 vowels
17 consonants
48 initial clusters
{11 unvoiced consonants, 10 voiced consonants, (m, l, n, and r get double counted) 9 "special exceptions": cs sc jz zj cx kx xc xk mz are all forbidden, and no double consonants}->191 internal clusters
gives exactly 20315 gimtai. This avoids only collisions of final vowels, and permits every other apparent "collision", including all those listed
in the CLL. These restrictions, to within a very crude approximation, probably divide the number given above by something between 2 and 3, giving a number between 6700 and 10000, probably closer to the former given that most of the collisions involve two letters. This is honestly pretty tight, to fit in ~1300 words.
I agree with you, though, that some fiddling with the gimste, doing things like changing final vowels to move further away from the source languages to avoid
some collisions would probably have been for the best. Too late now, of course.
An interesting computation: assuming every
combination of 2 vowels and 3 consonants can serve as exactly one gismu (which lets words differ only in their final vowel; not doing so makes the current number of gismu just
barely fit), you get 6800 possible words. Almost all such combinations work, too: ignoring the 9 special exceptions, any 2 vowels obviously work, and any group of 3 consonants will have at least 2 with have the same voicing. It might be interesting to make up a hypothetical gimste subject to this restriction and none of the restrictions I linked (but still the voicing rules and the special exceptions).
mu'o mi'e la latro'a no'u la latros