Well, mandagirl, the differences are so large, I can't even begin to describe them.
1. Even the largest pet store cages are WAYYYYYYY too small!
2. Fleece is much easier to clean and saves you hundreds of dollars a year in bedding. Here's a link about fleece and all the great stuff about it:
https://www.guineapigcages.com/forum/bedding/21568-fleece-project-study-24.html
3. C&C cages are much cheaper to make than a pet store cage is to buy. You can also custom fit it to fit in with your house. I built my 2x5 with a 2x1 loft for around $50. A pet store cage less than A QUARTER of that would cost almost double!
4. Fleece is MUCH easier to clean! Just vacuum the fleece twice a day to spot clean, and once a week, shake it outside, and wash it with unscented detergent and white vinegar. (No fabric softener. EVER.)
5. Since C&C cages are bigger, it's less work to clean, and the piggies can get more exercise, thus being happier and healthier. Happy, healthy piggies mean fewer, and less expensive vet bills.
The list can go on and on, but I'll let other users contribute some other ideas. I would really encourage you to built a C&C! On the homepage of the site (not the forum homepage) there are links about how to built C&C cages at home. All you really need is Coroplast or a shower curtain, zip ties, and SAFE grids. Here's a link to he site homepage for you to explore:
Guinea Pig Cages, Your Cavy At Home There is a box on the left hand side labeled " C&C Cages". Those are links to everything you could ever want to know about C&C cages.