One way drugs could conceivably give a different qualitative experience via a different ROA is if one route bypassed first pass metabolism where as another did not - so insufflated/plugged/IM/IV vs oral. If active metabolites play a role (and have different effects to the initial drug) then the overall experience could potentially be different if those metabolites are produced faster. Equally, if the main drug is the cause of the effects rather than it's metabolites, metabolising it more quickly could lead to a different qualitative experience in the same way that a low dose psychedelic or dissociative has different effects to a high dose. The latter theory would be no different to the effects caused by varying bioavailability however and I don't think it is relevant in the case of MDMA.
I don't know if any of this applies to MDMA or not but I was debating the same thing with a friend the other day - I have to admit I have in the past found that insufflated MDMA feels qualitatively different to oral MDMA but it has always bothered me and I don't know how much of it is due to the power of suggestion or conditioning. Logically, apart from a differing bioavailability and plasma level curve, first pass metabolism is the only thing I can think of that would cause an objective difference between the ROAs.
This falls down for me when you look at plugging however; the blood supply from the rectum bypasses first-pass metabolism (same as insufflation) yet it feels qualitatively the same as oral MDMA to me. I also freely admit I know very little about the metabolism of MDMA (quick google reveals that it is complicated and is an area of ongoing research, be interested to hear if anyone has anything to say about it) and I have a sneaking suspicion that first-pass metabolism wouldn't have a significant effect - especially given it's duration of action. One point in it's favour however is that MDMA usually metabolises fairly slowly, so if MDMA metabolites do play a role it is not inconceivable that first-pass metabolism could be important.
The other theory we came up with was that we only tended to insufflate MDMA when we were really drunk, so perhaps that has a bearing :D I vaguely remember skim-reading a paper about alcohol's effects on the metabolism of MDMA, but being drunk certainly can subjectively affect the qualitative experience of a drug.
Apart from that.. I am at a loss, sorry ali

I spent a long time discussing this with a friend at the weekend and I am interested to hear what others have to say.