Fanois,
This question has been asked a few times here before, and attracts various different arguments, however I can give you my opinion for what its worth
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Like yourself I studied Aero Eng, and finished back in 1997. The bottom line for me in making the comparison, is, it is simply different.
I too found the Beng Aero course hard and demanding. However, even though there were approximately 10 exams a year to pass, you also had the pressure of an excessive amount of course work to complete each term. I found this particularly hard to manage and found the whole process quite stressful.
With respect to the ATPL course, again it is demanding in the respect of the volume of information you are required to digest, however for me, it was a question of being able to manage your time constructively. Like most people here that give an estimation of the required amount of wotk you need to do for the ATPL's, it will take over you life for a good 6 months if you choose to do it full time. But that 6 months will fly by believe me.
On starting the ATPL course, I must admit I found it very useful having completed the degree course in Aero, due to the fact alot of the stuff I had seen before, for example, principles of flight, jet and piston engines, avionics, flight mechanics etc. However, at the same time I found my self learning alot too. Occasionally I found myself thinking 'oh that's what Mr X was on about at uni, never understood it until now'.
So, in a nutshell, like you said in your post, if you are willing to put the work in regardless you will reap the benefits and get a good set of results.
Good luck.