During the revolution the dethronement of the house of Habsburg was decided - but it was years later and not at the start (in 1707 and they elected for the throne Maximilian II Emmanuel of Bavaria). My point was it did not start with that goal in mind.
As for my speculations of the effects of Hungarian independence from the early 1700's:
1. Lets assume that Croatia remain Habsburg - with maybe the exception of the Eastern part. OTL the only parts of Croatia held by Rákóczi at any time were the territory around Osijek.
2. At the time of Rákóczi's war of independence the Bánát was still under ottoman rule. Though OTL Rákóczi had good relationship with the Ottomans im pretty sure that Hungary would try to regain this territory sooner or later - maybe in alliance with Russia. OTL in the Habsburg-Russian alliance the joint interest of wanting to conquer turkish territory was very important.
3. Hungary was devastated after the Ottoman era. It was subjected to 200 years of constant raiding with ocassional official wars - and Rákóczi's war was OTL very devastating as well - i read an account that put the OTL the death toll from just this to 20% of the populace. OTL the Habsburgs resettled the Kingdom with germans (most german in Transdanubia not alongside the austrian borders were settled at this time and a bit later the germans of the Bánát ) and serbs (a lot of them are preset by this time), and also from the less devastated northern part of the country (example: Slovaks around Szarvas).
ITTL germans might still be invited - especially if Hungary really ends up with a german ruler - but Im very sure that unlike OTL if there will be a german settlement it wont be confined to catholic germans.
4. The big one internationally: the war of Austrian succession. OTL the Habsburgs were doing pretty badly and without the resources or support from Hungary they might loose altogether. What's more if the Wittelsbachs are having Hugnary ad Bavaria in a personal union when Charles VI dies... We might see a Wittelsbach Empire encompassing whats practically OTL Austria+Bavaria. Against this becoming a reality is that not even the allies of the bavarians will be keen on the idea. Also without Hungary what would they find for Maria Theresia? Im pretty sure she even in complete defeat she would not be left without some throne.