There's one major flaw in the plugin change... Quite simply the 1.6 controller plugin was not designed for netplay in mind.
We (Gent, Pixii, Trotter, Ultramaniac64, Witten) gave hotquik's pj64k a thorough testing to see how it would hold up in netplay. While we were hoping for a fun time we quickly found several problems that were mostly related to the 1.6 controller plugin. When we switched to the 1.5 controller plugin most of the problems went away and the others received a nice shell bashing from yours truly

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The only remaining problems that remained were from the obvious lack of "proper" netplay support (sync issues mainly). Quite simply this is the main reason you dont see an official version of PJ64 with kaillera support from us.
Aside from that it seems there's a few other things that need to be looked at... While we're not directly affiliated to blokhed3 he is using the stuff we worked on. I dont think we were contacted to see where this would lead... Gent is very competitive when it comes to anything cheat related (as you can see in his post) and the rest of us wouldnt have minded giving it a quick testing to see if it has the issues we had noted before were still there or if anything was wrong with the packaging.
While 1.4 isnt too far from 1.6 there are several core changes that make most of the 1.6 stuff a bit troublesome for a "clean" transition, such as cheat codes, docs, and the rdb.