I have one of each, and they are very different.
Mind you, I think each ukulele can sound different, and play different, especially when you take into account different strings on each.
My Kanile'a was my first "real" ukulele. It has a boomy sound (that could be the bracing or the low g string though). It is the UV gloss, which is gorgeous to look at but does show fingerprints. It is super light (I think it is lighter than my Kamaka or KoAloha for its size). I don't mind the look of the bridge pins, but I absolutely hate changing its strings because it occasionally doesn't take on my first try, and I've had them shoot out and have the string snap up and cut me in the past. Not a deciding factor, but something to consider. Joe and Kristen are amazing people. I met them only once, but six months later they not only knew my face but my name when I saw them at the Ukulele Festival in Cerritos. I think they are beautifully made instruments, and probably the best looking ones of the big 4 Ks.
As for the KoAloha, I'm a latecomer onto the bandwagon, but I love my Pineapple Sunday. It has incredible volume (as does the KoAloha tenor that belongs to a friend of mine). I think maybe it is Papa KoAloha's background as an inventor that leads him to try new technologies and bracings. It is true, they are usually plainer looking koa and they are less radical looking now, especially with the new straight bridge -- though the Sceptre and PS and Jukulele are certainly unique. Their koa does tend to be straighter, and I think they kiln dry their koa while Kanile'a doesn't (I may be wrong on that though). They seem to be more techonogically advanced, and they have great volume. If you want a well crafted, loud, great sounding ukulele, you can't lose with KoAloha. I have only sent one email to them but it was answered by Brian, and Paul is great about writing on UU and so forth. I think they have the best warranty, as evidenced by the fact they have even helped "second owners" with their ukes. I agree the headstock is flashier, and the musubi sound hole is less traditional, but the rest of the uke seems more traditional than some of the flashy Kanile'as.
I think both companies actually have better customer service than Kamaka. Don't get me wrong, I love my Kamaka to death, and they were lovely people when I did their tour last year. But I think they coast a bit on their name and reputation. KoAloha and Kanile'a being the number 2 and 3 kids on the block seem to try harder. As a result, they both have incredible customer service, so I wouldn't let that be a factor.
I know this didn't help you at all as I sing the praises of both companies, but you can't go wrong with either.