In Denmark most major commercial sites use a system from RedSherrif that is scripting based too. I have used it in my work for some of the big portals here and I can only agree to what have been stated before: I sucks (sorry, but it do!)
1) You need to be 110% sure that you have ALL pages correctly tagged. If you miss one then the stats from that page is lost forever. There is no way to get it back. I have yet to se a single major site that can prove a 100% tagging rate - even with an agrssive "syntax-crawler" on a 24 hour hunt for mistakes. There will ALWAYS be mistakes.
2) The script add another server connection to each page. If you run banners too (usually from some kind of ad server) then you have at least 3 connections for each page. If just ONE of the servers is down or slow then that pages will stall. More server connections = more headache :-)
3) If the service provider you use mess up the system then you loose valuable stats. Even with RedSherrif (that is NOT cheap!) this happends now and then and when it do you will be loosing important stats for the day. If that day is in the middle of some campaign then it can be very "expensive".
4) Usually these systems is only updated every 3 hours, so you will never get "real" real time stats this way. Even though you dont need real time access to logs or stats every day, now and then it is nice to be able to pull last minutes logs if you need it.
5) You only have the repporting types that THEY choose to set up. You can't define new repport types or change or manipulate them in any way. Not even the small things you can do with WT is possible here :(
I only see one good thing about RedSherrif the way we use it in Denmark: We all use it! That way you can compare stats from one site to another - not from guessing, not from a panel, but from all the real traffic.
You can see the Danish stats here:
The way I see it, RedSherrif - and most similar trackers - are repporting tools used to run official stats. That's what it's good for. It is NOT a traffic analysis tool. You need far more flexibility then what it provides - if you ask me, that is ... :)