The reason for merging IP with Blue Essence
Before preseason, IP and BE were separate, though they were linked in that players could buy Hextech Mystery Champion Shards to convert their IP into BE. IP's primary function was to unlock Champions and Runes, its secondary function was to unlock cosmetics (like name changes, Chromas, and for awhile, Summoner Icons). BE's primary function was to unlock Champions, its secondary function was to unlock Mastery Levels (aka cosmetics). With Rune prices going away in preseason, IP was going to have one primary function, unlocking Champions. Thus, both IP and BE would be currencies primarily used for unlocking Champions, secondarily for unlocking cosmetics. Both currencies would accomplish basically the same things, so Riot merged them.
Why did Riot keep BE over IP? Whichever currency they kept, it had to be connected to Hextech Crafting. Riot was not simply going to do away with its entire Champion Shard system because that would mean major changes to how Hextech Chests would work. Blue Essence was already connected to Hextech Crafting, so Riot decided to axe IP by converting all existing IP to BE and giving players more Champion Shards to disenchant in place of IP.
Merging the two currencies meant that whatever IP income that players got through playing matches and whatever BE income that players got through Hextech Chests were combined. Because prices for BE items (enchanting Champion Shards and getting Champion Mastery) were based on players earning very low amounts of BE over time, the BE prices had to be adjusted since players would be earning BE at much higher rates once IP was merged with BE. Champion prices feel relatively acceptable because the IP prices were just converted 1:1 into BE, and we earn BE at about the same rate* as IP.
The reason why Mastery costs feel so bad right now is because of the same reason why it was encouraged to spent money on Hextech Mystery Champion Shards before preseason. The BE value of each Hextech Mystery Champion Shard was higher than its IP value. By buying Hextech Mystery Champion Shards to get Champion Mastery, you were essentially making your currency go further. Riot did the calculations; you were getting about 6.5x more IP than you did BE. That's why they chose to multiply your BE by 6.5 and it's also why they chose to multiply the Champion mastery prices by 6.5. (500x6.5=3250 BE, 600x6.5=3900 BE.) It should feel the same, but it doesn't, and that's because you no longer have the option to increase the value of your currency anymore by converting IP to BE. You're just stuck with BE with no way to make that BE more valuable, and that's why the mastery prices feel bad.
It's not all bad though! You're getting more Champion Shards than before, and it still only takes one Champion Shard to increase Mastery Level. Thus, you have a lot of chances to use your Champion-specific Champion shards to increase mastery. Additionally, since you're getting more Shards, you're getting more chances at being able to enchant them and get a Champion at 20% off. It just depends on whether you're willing to wait for the Champion Shard of the Champion you want, which can feel bad.
*I am not trying to get into a debate about the rate of BE earning. This is not the point of the post.