Personally, I think each application has it's place. Sure, I've created layouts complete with vector graphics in Photoshop, just to prove a point, but in the real world you can't do that. The person doing the prepress work on your files will probably be used to doing things a certain way, and if they're not experienced enough, they may do things wrong if you use unusual applications.
In one of the companies I work for (a digital printing company), we have three ways of planning up a job: We have an XTension for QuarkXPress which came with our press, and is probably the easiest way to work. Secondly, we have a plug-in for Acrobat, which is pretty good too, and allows us to accept PDFs with no problems. Finally, the RIP itself can impose jobs after they've been RIPped, but it's not very user friendly.
In that scenario, EPS files have a number of options. For example, they can be imported into Quark, but that's dependant on the prepress guy being careful with placement.
They can be sent directly to the RIP, which then makes it difficult to collate. Also, if the bleed is assymetric, some RIPs may interpret it incorrectly.
Having said that, it is possible to use Illustrator for simple layouts, provided you're careful, or if you know you can trust your prepress people. My personal experience is that people who supply Illustrator page layouts are generally going to cause problems, and while it's a view that others share, I appreciate that some people don't have a problem at all, so check with your printer. I would add, however, that we had a guy working with us for a while that didn't agree with me, but over 70% of his Illustrator jobs were rejected (he brought them into Quark, but didn't place them properly).
As for PDFs, I would say that, provided they're set up correctly (with bleed and embedded fonts, for example!), there shouldn't be a problem. All good printers can use them, which is a good thing, because it means that it's becoming irrelevent which software you use to create your files. It's certainly more pervasive than InDesign, but ID can create amazing PDFs, so it's not really a problem!