I have frequently cited the difficulties of balancing a game in which the players have upgrades. Either you assume that players will be mostly/fully upgraded, in which case the base content is nigh-impossible without them, or you balance it so that players can beat it without grinding in-game cash for upgrades, in which case it will be face-roll easy for anyone upgraded.
The clearest example I have met yet is Notebook Wars. Flying into the last mission without a fully upgraded weapon, the final boss took 15 minutes. Its attack pattern is about 5 seconds long, so you might imagine those were not the most exciting 15 minutes of gaming I have, but you know the bloody-minded need to finish it when you’ve gotten that far. For bonus fun, the shots you dodge in that fight have a slightly larger hit box than the graphics for them.
There is a downward spiral to this. I upgraded for defense before offense. The cash for upgrades comes from killing things, not surviving or beating missions. On the second row of missions, I saved up for the best ship (defense), so on the third row, enemies were flying off the map before I could kill them. It was ridiculously easy because I did not need my new ship’s increased speed; its increased hit points let me turn on autofire and go AFK during the level 11 boss fight. (That fight, by the way, would be a great place to farm money if you were so inclined, because the boss spawns enemies that are worth a lot.)
Or maybe the designer meant to have a 15-minute long boss fight on the idea that really long fights are epic.
[Update: the latest Zero Punctuation addresses this same topic in a game that has a budget.]