Yes, there are plenty of EE3 conversions that are going to be controversial---the entire mod is premised on a single person establishing a game-wide economy for the lossless conversion of dirt into everything---but the topic of this thread is on the most illustrative example of EE3-gone-wrong: The absurd idea that four Iron Ingots are in any way "equivalent" to an Ender Pearl.
This makes no sense from a mechanical perspective, from a thematic perspective, from a "plays-nice-with-other-mods" perspective (which pahimar should be very cognizant of---for shame), or---most damningly---from a balance perspective.
Mods use items like Blaze Rods and Ender Pearls as balancing tools, relying on their rarity to prevent the abuse of abusable mechanics. Consider RailCraft's World Anchors, which require Ender Pearls as fuel to limit server load. Consider Thermal Expansion's Liquid Tesseracts (or Ender Chests), which can provide infinite MJ and infinite EU via Nether lava with very little infrastructure. These mod authors chose Ender Pearls---not four Iron Ingots---for a good reason: to limit the impact of these powerful features.
And then EE3 comes along, and utterly kills the Ender Pearl as any sort of balancing mechanic whatsoever.
Ask yourselves: What do you have more of? Gold or Ender Pearls? Diamonds or Ender Pearls? Even better, multiply your stock of Ender Pearls by four: How does that number compare to your stock of Iron Ingots? Any one of these questions should starkly illustrate how absurd a 4:1 conversion rate is. Perhaps more viscerally, what makes you groan the most when you see it in a recipe: four Diamonds, or four Ender Pearls? What about four Gold Ingots vs. four Ender Pearls, which is the actual EE3 conversion rate?
I've heard that the only reason FTB lacks a direct MJ-to-EU conversion device is because a balanced ratio for conversion has yet to be found. This reasoning strikes me as patently absurd when the same pack includes a mod that enables infinite energy of either type at the mere cost of a few Iron Ingots.
Equivalent Exchange 3 MUST incorporate abstract costs---such as the difficulty of acquiring one item over another---into its equivalency mechanic. Failure to do so will rob other mods of the ability to control their powerful features by requiring rare items; rob the game of hours of play by making numerous objectives redundant (e.g. building an Ender Pearl farm); and rob FTB as a whole of any hope of holistic game balance.
In my opinion, "4 Iron Ingots = 1 Ender Pearl" is, without exception or qualification, the biggest black mark on the FTB pack at the present time. It is the only component of the pack I do not use because I consider it cheating.
Edit: Just as I finished typing this (while idling in my base), an Enderman bamfed in right next to me. I killed it. No Ender Pearl. DAMMIT.