How much of a NO-NO is it to put supply ducts at the end of the supply
plenum? We could use better air flow at the ends of the house and I was
wondering if the larger plenum with all ducts to the side would help.

Simple laws of physics always work. You want more air flow, use larger ducts.
Too many HVAC installers make tidy looking installations that disregard simple
rules. Maximum airflow depends on plenum and blower design and should follow
manufacturer's recommendations.
Your post will likely trigger many responses from HVAC experts. Some may have
practical advice for your situation. You may even need to talk to one or more
other contractors to arrive at a logical conclusion. Good luck.
Joe