You can look for wear indicating a lot of use. You said it was "tight" and if you are referring to the way it breaks open, that is usually an indicator of a gun that has not been shot enough to break it in good.
Also look at the top lever with the gun closed (check both barrels). The lever should be to the right of center. If it is in the middle or to the left (with either barrel), the gun has been shot a lot and needs service. That is no reason to turn it down if the price is right, but it may be an excuse to talk the price down. The last time I had that kind of service done to a Beretta it only cost about $100 and it was as good as new (prices may have gone up since then).
Ask the guy where he got the barrel with the non-matching serial number, and (most importantly) if he had it fitted to the gun by a gunsmith. Often they will go on the gun and appear to fit OK, but if they are not properly fitted by a 'smith the result is faster wear.
Shoot doubles with the bottom barrel first (one red dot showing on the barrel selector) and with the top first (2 dots). Any failure to fire the second shot means some work is needed, but that only affects the value, it is not a fatal flaw. It is nothing that can't be fixed.
You said some choke tubes are missing. Factory flush tubes are cheap, and you can often find them on eBay, although the 28 ga ones are not common.
The lack of the original case is unfortunate, but not really important. It probably wouldn't hold both barrels, anyway. WalMart has cheap ones that will take both barrels and are strong enough. But again, the lack of choke tubes and case are reason for talking the price down.
Small wear spots in the bluing are easy to touch up. Other than that, it is hard for me to tell you how to evaluate the condition as far as dings and scratches are concerned. You do need to look for dents in the barrels. They can be fixed if they are small, but they affect the value.
Right now I can't think of what else to tell you. Good luck.