oh definitelyy, if claire hadn't left, season 3 would've looked very different from how we know it - for one, the whole storyline w rikkiβs cafe and rikkiβs conflicts w zane seem like it was originally written for emma and ash. ash was stated to be working towards a business degree (if i remember right), and he was the manager of juicenet cafe - it makes more sense that he wouldβve bought the cafe, instead of zane, and named it after her (thus it would've been emma's cafe), and put her in the managerial position that she wanted in s2
it fits that the conflict rikki and zane had in s3 was supposed to go to emma and ash - the zane i know wouldβve never held the secret over rikkiβs head or threatened to reveal it or disregarded it like that just for his friends - but ash on the other hand, was shown to be very pushy, literally showing up at emmaβs house and barging in, tried to force her to go in the water despite her protests, etc, eventually reaching the point where she felt pressured to tell him her secret (which imo is not how you want to start things off at allll in a new relationship)
given the tension between rikki and will, and zane's jealousy, it seems like they were also setting up will to be emma's new love interest - she would've been the one to save him instead of rikki, and would've been viewed as an "angel," (paralleling zane calling her a sea monster in s1), and ash would've been continuously antagonistic towards him
rikki and zane probably would've still had their roles to play with the cafe - zane might've been a sponsor for ash and the reason he was able to buy the old juicenet cafe to begin with, given he's pretty rich, and his dad would've still pushed him to get involved in business, plus he and ash were getting pretty close in that one episode. he would've had more of a role w helping in keeping the secret, been not an antagonist and more involved in trying to fix problems instead of the other way around
and rikki could've gotten involved in the band, whether it's alongside lewis and bella or instead of them - some of the show points to her interest in music (the ipod that zane got for her, her listening to music w her earbuds in as she's going to sleep, going to a concert, sharing the same music tastes as lewis - who also joined the band)
i'm not really sure what much would change with cleo's storyline, some aspects would've probably still stayed the same, like her becoming a dolphin trainer - but lewis, though, i think since he literally had a vision of cleo's tail being revealed at marine park with too many of the details being the same for it to really be a coincidence - he probably would've prophesized mako's destruction instead of the tentacle revealing it to them, and the comet was probably not the reason for the island's destruction, but rather harrison trying to build a resort on mako like he was planning in s1 - a full-circle moment for the show
if bella was still included, she might've been a more sophie-like character - she was probably supposed to be s3's antagonist, given sophie's actress played julia in season 2 - julia probably would've had some backstory in s3, but claire leaving the show meant things were shifted around so they had to get rid of julia's storyline to make space
tldr; emma was very centric to s3 and claire leaving changed literally everything as we knew it