EMV are the chips in the cards, something coming to the US later this year. Canada already has them. PCI are the rules for credit card security that you agree to when you setup your merchant account.
Not knowing how big the system you're getting is, I can't say whether it's worth $5k. I think realistically, you should plan to spend more than a few hundred dollars on installing, programming and training on it. Plus it does need to be licensed. So let's say you end up spending 10k altogether on it and don't relicense it. It's a used system, probably running XP or older seeing as Micros is already suggesting you replace some of it. You probably won't be able to do CCs on it unless Micros will change the software for you. You may get a few years out of it, hard to say and if you really know the software, all the better.
If you spend the $23k with Micros, you will likely get about 8-10 years out of it, a warranty and I would think training and programming was within that cost. It isn't really all that bad a deal but if you're going to spend that, you should look at some other systems. You might be able to get something for $10-15 and still get the 8-10 years out of it.