Carlos Im not attacking you - but what you ask explicit has nothing to do with dvd2one - you say so yourself. You are not content with the quality of dvd2one under certain circumstances and need advice on some other way of reencoding that will give better quality. This is all very well - I do understand your question - but since this forum deals with specific questions about dvd2one you will propably not get to many answers here.
Instead you should look into one of the thousands of guides on the net explaining how to reencode using other tools, like cce, avisynth, tmpgenc, etc. etc.
Google is a very good searchtool for this
http://www.dvdrhelp.com is a place to start for instance - they have alot of guides and information about your subject.