We've just moved over to InDesign and its just so much better than Quark - printings a doddle, the built in effects have reduced the amount of time we have to use illustrator and photoshop and I can really say its been the best investment we've made recently.
I don't think it'll cause a problem as so many people are moving over to it - the only people not so keen to move over (in my experience) are some repro houses who have problems with the rip outputting the built-in effects like text dropshadows over images etc. A few want to stick with Quark cos they know how to get around rip problems whereas InDesign would mean re-learning an InDesign for its outputting limitations and work-arounds.
PDFs are certainly more accepted at repro houses but some do still have problems with those effects etc.
On the whole I'd say stick with it - Quarks a dog in comparison!
Just my 2p!
