Well It depends entirely on the sort of customization you're doing - and the aim of the SharePoint solution.
- Fairly obvious, you've got your own branding on the site rather than the default OOB.
- Depending on who you ask this can help provide corporate identity, make people more productive as the interface may be more familiar, and many more design-related aspects.
- Vary a little more.
- SharePoint customization can be a little quirky, and it's easy to accidentally break functionality with more dramatic customization.
- Upgrades may cause other problems, though I've never had that happen.
- The final problem, and biggest I've encountered, is that once people realize how much the interface can be customized they tend to ask for more and more specific changes. Whether this is a good or bad thing depends largely on whether you have the time to make several hundred little tweaks on individual site collections.
Overall I'd say branding is definitely worthwhile, and very unlikely to cause problems. Major changes to master pages need to be more carefully considered and should have a very strong justification before going ahead.
Reference by James Bore
For larger organization, its up-to them how actually they want. For them it's like they have multiple sites collection, sites etc with different kind of UI. so they have to invest more to customize all the site collections, sites, pages etc. so they prefer out of the box UI.
In my career I have customized so many masterpages, It was always challenging.
The way it gives an output is what customer wants.
So even after Microsoft doesn't recommend to customize the masterpage, I would always prefer customizing masterpage whenever its required.
Hope this brief helps you!