I played through 3-6 of the series and personally felt that it ended on quite a fantastic note. They consistently evolved the core gameplay by adding new and different features each game(style changes, soul unisons, dark chips) and the constantly expanding chip library really gave it the feeling of endless exploration of different play styles.
I have no sales figures to back this up but I believe the series was still doing quite well all the way till the end and the series was ended simply with the end of the lifespan of the GBA, migrating to the DS in the form of Megaman Star Force(which introduces larger changes and I feel remains strong entries in the franchise that got unfortunately got weaker)
Getting lost in the dungeons was definitely a thing, and even more so as the puzzle design of the dungeons evolved in 5 and 6, definitely still fairly simple with some effort though. Overall I think the series finished strong and narratively wrapped up quite nicely as well. I highly recommend you go back and revisit the later games in the series(5 has a weird turn based strategy element while 6 probably presents the strongest example of the dev team's vision) and possibly even the DS series if you have even a passing interest in the series. The action gameplay style definitely still holds up.