UEFA doesn't want to improve Europa League or even Conference League. In fact the new format was to collect more money and make new teams in these two competitions win titles rather than the classical teams. There is a positive points is to boost the funds of the teams participating in these competitions and help them improving the squad so a long term improvement in the quality of teams especially from lower leagues in Europe. Obviously in short term no direct benefit will be seen.
You made some good points about how UEFA handles Europa League and Conference League. Many people think money is main reason for changes in football tournaments and these new formats look to be no different.
It is interesting to suggest that new rules are meant to help new teams win instead of usual big clubs. However bigger prize money and other payments could really help clubs from smaller leagues or those who do not mostly play in Champions League. As you said this extra money can help them get better players and grow over time. This will make European football more competitive in future. You are right that we will not see quick benefits. Improving team takes time and effects of more money will probably show up slowly.