You forgot Team Rocket popping up somewhere along the line to steal Pikachu as the third act of every episode.
I don't know how much the actual format was at fault, but the travelling episodes eventually felt very empty because of this. The twerps started to feel like chess pieces doing the same thing every episode, mostly reacting to new stuff around them and the formula not allowing them to deal with anything differently. Formulas can work if you let the characters be versatile enough to make it fun and different every episode, but while the show started off like this, by parts of AG and DEFINITELY by XY the format was pretty much like trapping them in tiny boxes and forcing them to say the exact same lines over and over by gunpoint. Not even the most charismatic and multi faceted character can avoid looking bland and boring this way.
With the standstill format, it at least feels more often like the they're the driving force of everything, especially since the premise demands that THEY make it different, along with the fact they can have closer connection to the scenario (eg. their parents or guardians or homes).