The installation and upgrade process can be a bit quirky at times but that is to be expected with the amounts of data involved.
The 2 stage installation process may confuse some and on old sites which have been migrated from J1.0 to J1.5 to J2.5 problems have been encountered.
On a busy site it will store a lot of data but the ability to choose and remove historic data is without doubt to be welcomed.
The interface may confuse some as some of the views are similar but different.
The ability to classify a visitor as a bot has helped increase the accuracy of the statistics when comparing them with Google analytics.
Yes there are minor issues but in our experience there is nothing even close and we would not like to think about managing our sites without it.