ProSalesforce has a better report writer than RE - you can work with pivot tables without having to resort to Excel, and you can put two reports side by side for comparison. You can create graphs and display them in a given constituent record, again without having to use Excel. (RE does have graphical dashboards.)
At the moment I'm uploading and downloading tens of thousands of constituent records, and SF performs much better than our on-premises SQL database.
Data loader can be run from command line.
There is much more customisation possible with the layout of the page. This is particularly useful as a page can be quite long, so you can hide sections that you never use.
Duplicate checking is better than RE's since they "improved" it a few years ago and it got worse.
Global search across lots of fields.
ConsYou only get 1Gb of storage, without having to pay more. I appreciate that it's not quite the same as 1Gb of RAM in a desktop PC, in that it's replicated, and backed up etc. Still though, that's not a lot of space for storing your data.
You're using a web interface, which doesn't have the slickness of a native app. I suspect when it comes to data entry people are going to have to be switching between keyboard and mouse a lot. If you start tabbing to try and get to the first editable field on a page, it's going to take a while.
The data loader doesn't let you validate before adding data. You just have to run it and then fix the errors in the records that failed. (Other dataloaders are available, I haven't investigated yet.)
The data loader tells you of duplicates, but doesn't tell you what other record looks like a duplicate.
Causeview documentation isn't very complete. None of the context help I've tried has worked.
Gifts are split into three parts - transactions, payments and allocations. So you don't have to click between tabs on an RE record, but you do have to click between pages in order to find out information about gifts.
Objects have names which aren't very helpful. For example, Funds have names like F-01768. They have a description, and a separate fund code, which we set to the names and codes we've been using previously. However throughout the interface, if it's going to display one thing, it will choose the name, which is pretty meaningless and can't be changed.