The main reason I prefer Nessus is that it produces better results. Also, when you are analysing the results, you have an option to see only the vulnerabilities for which "Exploit exists". This is extremely useful. In Nexpose you can see the ones where you have exploits in Metasploit and in exploit-db (very useful and not present in Nessus). Also, in Nessus you have the mention that a Metasploit, CANVAS or Core Impact exploit exists. For the rest you have to search the net.
Among the false positives in Nexpose, the most annoying ones where the ones detected when I executed a scan using admin credentials. As an example, for one server it reported a browser exploit. In Metasploit the exploit applies to IE 6, but our machine had IE 8. Another one was valid for Win 2003 SP0, and our machine wasn't for sure SP0.
Last year I did a comparison between the two vuln scanners using regular network scans (without credentials). After the scan I tried to identify as many as possible false positives. The results from Nessus were much more accurate, and Nexpose missed a lot of vulnerabilities.
Another disadvantage of Nexpose is that if you enter for scan a class C, it will consume 255 ips (from a total of 1000 in my case). Because we are using many subnets I would have to do a scan with Nmap first, and then import the results in Nexpose. I think that sometimes, when you do this, it will erase old entries.
The advantages with Nexpose are the facts that you have a nice management of the zones and extra scan engines, and that it produces more detailed reports, that gives detailed remediation steps.
For a big company the management of zones and scanners is a plus, because the Tenable Security Center (necessary to integrate the results from multiple Nessus scanners) costs 80.000$. So, if you have many zones, with many scanners and you want all of the results in one place Nessus vulnerability scanner is not the solution to go. You either buy Tenable Security Center, either go for another solution (Nexpose being one of them).
In our case, we have a scanner internally, one in the DMZ and another one on a machine connected directly to the internet. With Nexpose, the first two could be combined, and have all the results in the same place.
I didn't try yet the integration of Nexpose in Arcsight, but I might try before our license expires.
And, yes, the price is important for me. Scanning 2500 real IPs (and I give him ranges that will cumulate almost 10 000 IPs) with Nessus costs us 1200$/year. With Nexpose will cost way more.
Worst, we have Nexpose through Symantec, which resells it as CCS. When you have a problem, and you need support, you have to deal first with Symantec, and when they are not able to fix the problem, they will escalate it to Rapid7 (which gave me the solution very rapidly).
Maybe I am biased, but this is my opinion. If you want, I can provide some tables with the results of two scans. My analysis is not 100% accurate, but there is a big difference between the two scanners.
CISSP ISSAP, CISM/A, GWAPT, GCIH, GREM, GMOB, OSWP