I don't really see how the route would be that much harder.
forest1 - easier. awkward movement to and from sword and over the fences has been eliminated.
escape - harder. there are setups for naviless w/ stick because of no WW route, but most are slow. Coming up with an optimal one might only be a matter of time, or you could just move back slightly instead of slashing the wall and hope you don't break your stick as you clip. also, there's always setupless Kappa
river - easier. no more timing based red rupee strat. not that this strat was particularly difficult, but it just got easier. since you can't superswim from the waterfall, you don't have to worry about the WESS to hyrule field anymore.
wess to kak - easier because stick is longer (you have to press stick twice I guess but you can just mash)
cuccos - easier since you can't do the slash at the end, so you have more control.
mido skip - same or harder. i can't really comment on this, but i imagine it's harder since you have to draw the stick before JSing.
deku - can't go for the precise sword strat for vine text skip. the timing for b1 skip might be different, but it should be the same difficulty.
I'm not sure what the deku route is, I would guess that you get a stick from one of the babas on the way to the 1st vine, and maybe nuts as well, or maybe you get nuts after b1 since you already have broken stick out to kill the baba, and collecting the nuts sheathes the stick so you can shield for scrubs. It's hard to say whether deku is harder or easier, but maybe it's just a matter of time to work out new strats and practice them.
gohma - same unless you try to save 1-2 seconds by moving before ISG, but that doesn't seem worth it anymore. If this route is faster, it might be worth omitting that anyway.
ww - i think itsjustindt modified the zas setup so it works with stick.
I have no idea about rupee route at the moment.
