update: Gmail vs Google Apps – Which one is better for personal email is an in-depth article that answers exactly what I wanted to know. (Although "better" is in the title, the article mainly states factual differences between the two.)
I'll move this to an answer if this question gets enough votes to be re-opened…
I currently forward my Google Apps Free edition (legacy) to my classic Gmail account. This way I can use my custom domain email address from Gmail. I do not use Google Apps as my primary account because in the past Google Apps often lagged behind in features. However, is this the case anymore?
I found a comparison of the different editions of Google apps, but no recent comparisons between Gmail and Google apps.
Whether or not something is a 'downside' would be a matter of opinion and can vary from person to person.
However I can say that Google Apps does still lag behind consumer Gmail for some features. For example Inbox came to consumer Gmail several months before it was available in Google Apps, and Google Spaces currently can't be used by Google Apps accounts.
Having said that, there are a lot of controls, settings, and 'upsides' to using Google Apps. Some of these include making Google Groups (with their own email addresses) and aliases for your Google Apps account at no additional charge.