For fermentation, you will need an external controller regardless of which one you choose.
Upright
Pros: easy to load and makes good use of vertical space. Ball lock kegs are a little taller and narrower than pin locks, so ball locks are a good candidate for uprights. Uprights are very common, easy to find, and cheap if you shop wisely.
Cons: configuration typically requires two rows of kegs, one behind the other. Shuffling kegs around can be a pain.
Chest
Pros: makes great use of horizontal space. Even a modest sized chest freezer can hold quite a few kegs in a fairly small footprint. No shuffling of kegs required - all kegs are accessible at all times. Because they are designed to freeze, they typically have better insulation and are cheaper to run at fermentation temps.
Cons: Requires lifting kegs over the edge to load. If you ever plan on using carboys, this can be particularly dicey. Chest freezers are harder to find and may be a little more expensive. Shop around, this may be a non-issue.
Prosit!