Plus was originally written at least 5-6 years ago, by somebody that was knowledgeable about video. Whie it does also offer a "dummy" interface (the wizard and templates), it gives you an incredible number of options. Many of those are still not found in professional MPEG encoders.
It's actually kind of sad that TMPGEnc is a lesser quality encoder than Procoder, for example. TMPGenc Plus has a lot of untapped potential.
The new TMPGEnc version, like XPress 3 and 4, are written for impatient video newbies. It's all wizard-driven, and in some cases you get less filters/options than were found in Plus 2.5. The biggest advantage of the newer versions is it natively accepts more video formats, no more playing around with environmental settings to juggle codecs.
As far as encoding quality, nothing has changed. It is still slower than others, and it still requires more bitrate than others to achieve the same quality (compared to Procoder, MainConcept
Personally, I like the tried and true TMPGEnc Plus 2.5, there is nothing wrong with it at all.