I see wide variety of proto boards for sale: some has green soldermask and plated vias in a grid, some is just brown with holes in a grid. Pros or cons to either variety? Stock photos attached.
If you're talking about high quality name-brand protoboard, Ledtester's list of pros and cons applies in its entirety, and I'd say that both are good choices.
If, however, you're talking about getting protoboards from China (eBay, Aliexpress, etc), then I strongly suggest avoiding the brown ones, as the quality of those from China is abyssmal. (I got some with missing drill holes and terrible etching that had shorts between some pads and breaks on some traces. The quality was like a poorly done homemade PCB.) In contrast, the fiberglass boards (green usually, but also available in other colors) are excellent.
You can also find non-plated-through-hole fiberglass perfboards on eBay and AliExpress if you look a bit harder.
And also consider designing your own perfboard and having it manufactured in China — it's more expensive but still dirt cheap, and you can have them however you want!