Some things I feel are important...
Menus: ISC menus suck and I have an obscene amount of menu items that I simply can't get rid of or re-org. It would actually help me to add more. CS-Cart has those useful top menus where you can have a ton of sub categories and it looks and works great.
Layout: This is going to be the biggest determining factor. I have to say that I think I have the baddest looking site known to man.

Mobile Version: I was pretty appalled that CS-Cart charges a monthly fee for a front-end mobile version of this cart (when you have over 1000 products). Why should that even matter when you aren't displaying them all at once anyway? It concerns me greatly actually. This is also a deal breaker. If I can't find a way to have a mobile version of the site without paying a monthly fee then it's a done deal.
Plug-ins: I can already see by the plug-in prices I've been seeing that I'm going to have to learn how to code plugins myself with CS-Cart. I don't mind paying for plugins but not at the prices that I've seen some of the CS-Cart plugins costing. It reminds me of the high prices charged for ISC plugins but in all fairness to ISC programmers, they were doing it with no documentation or support and having had to do some coding myself for ISC, I feel it took 10 times as long as it should because time had to be spent understanding ISC from a programming perspective with no help. The most coding I've had to do with ISC was for layout features CS-Cart already has. The other coding I've had to do deals with interfacing with my supplier's servers for real time stock level updates. So it would be nice to be able to make one plugin for that instead of going through all the core files and manually adding this.
So pros that I see with CS-Cart...
1. *A database that doesn't have data all over the place.* - after more looking, this is no longer a valid statement. Product data alone is spread out in tons of tables.
2. DOCUMENTATION - this should be #1 but I'm too lazy to re-arrange the list.
3. More functional menus
4. Pretty much all of the basic and many of the advanced features of ISC
5. Plugin system with DOCUMENTATION so I don't have to edit core files (hopefully. I'll know more when I get into it).
6. Built in Affiliate program. I do need to check to see if I can integrate the cart with our Share-A-Sale program, so this could be a deal breaker as well.
7. Built in Newsletter abilities. I have to look more into how the newsletters are sent but it's a good start to have it integrated
8. API documentation so I could quite possibly write WordPress plugins for it., ie. product widgets & embedding links to the products into posts automatically by typing the product name, etc.
9. Reward points
10. Events - love this feature. When we start hosting more on-air radio events and what not, this will come in handy.
11. SEO links. It's nice to have this natively and sucks that I spent $150+ to have this feature in ISC and not without a heavy core mod.
12. Easily disable countries and easily force billing to be the same as shipping address.
Wishlist
1. I haven't completely let go of the idea of giving store credit so I wish that feature was still available so I could use it sparingly. Although I do like the other options CS-Cart has for comping customers, ie. gift certs,award points and free gifts.
2. They should have a facility for Brands so people can search by Brand. I see they have suppliers but to me that's something different. I'm hoping brand is a searchable feature by some other means that I've yet to discover.
3. I doubt this will change but I wish most of the important product data was in one table. Right now it's spread over several tables and will make writing code to create a datafeed for my affiliate program uglier than it needs to be... same goes for our quarterly mass price updates too.
UPDATE: I don't know... I think I'm back to passing this cart over again due to the mobile template issue. Doesn't seem to be a less ridiculous solution at the moment.