MFR is all about automation - set and forget machines that do all the work for you and output it's products in a fairly straightforward manner to your sorting system of choice. All it's machines are relatively cheap and simple to put into operation. Not much more is needed, just a way to pipe items out and sort them, and enough power supply. For many people, that makes it a boring mod. Multifarms are much more high-maintenance, but are more effective power-wise. They yield multiple byproducts instead of just Saplings from a tree farm, and you have to deal with these byproducts or they might choke your system. To automate them you have to go to much more work than you need with MFR... For full automation, you need an autocrafter of some sort to automatically produce Fertilizer for you, and a way to automatically mine more Apatite so you can continuously use your machine nonstop, as well as a stable powersource - with the advantage it can be a very weak and low-maintenance power source, since they only require a constant but small amount of MJ's to run. Let's also not forget that Forestry nerfs vanilla saplings in terms of ethanol production, so you have to get into tree breeding if you want to be a little more efficient about it. Sure, that made lots of people drift away from forestry and go easier routes of producing renewable power, but does that make the mod obsolete? No, and i'll digress some more about it further down.
Like Hoff said, MFR is more power-hungry and that supposedly balances out the easy automation it is able to deliver compared to other tree farm designs. Back when Extra Biomes XL was the standard instead of BoP, i preferred a turtle farm with 2x2 Fir Trees to supply me with saplings for biofuel, and wood for charcoal to use in solid-fueled boilers for power - Fir Trees specifically because they were really tall, and because the saplings for some reason did not require unobstructed line of sight to the sky in order to grow - so a new tree could be planted and bonemealed into a full grown Fir Tree just after the turtle had finished cutting down the other one, also the amount of leaves produced silly numbers of saplings as well. It worked wonders - the amount of fuel produced was far higher than what the turtles consumed and that made me happy. Nowadays i feel it was kind of cheap, just like using turtles for quarries. You can have a turtle-quarry + turtle tree farm in less than 10 minutes of gameplay. Just use your first three diamonds to make the diamond pick for the mining turtle, download the program, put it to run, and forget it. That's why i stopped using it. After the first turtle quarry i could place 10 more turtles with the resources the first gathered, and that made minecraft too easy.
As for the answer to the OP:
Sometimes going the overcomplicated route is more fun than the straightforward and boring automation you've been accustomed to for the last 10 or so worlds you've played. Once i "gated" myself out of just using turtles for nearly everything since they're as cheap as they come and i can just download programs other people have made, i started really enjoying the variety that exists inside a modpack, and making my own programs whenever i did want to use a turtle or a computer. I started trying out all the other possible automation. I started enjoying manual mining again after Tinkerer's Construct gave me the Hammer. I tried to make a sorting system with only Thaumcraft golems, and failed epically. I started playing around with other mods, and started to actually really enjoy what a modpack really is - all the possibilities it gives you, and the challenges each one brings with it.
So i think the problem is not how far is too far with automation. There is no limit to how much you can automate things. Hell, VSWE's new Factory Manager mod makes automating everything a hell of a lot easier. The problem is when the same kind of automation is all you've been using for the past 10 or so worlds and you're bored with it. So you get out of your area of comfort and go try out some new mods and new ways to automate things. Got tired of using Barrel-Sorting? Go AE. Got bored with AE? Go try out Logistics Pipes. Got bored with that too? Try out ExtraUtilities sorting. Got bored with that too? Try automating things with golems. Got bored with that? Try making a vanilla hopper sorting system. Got bored with all of that? Go check new mods on the minecraftforums and try them out too. Minecraft places no limits on your creativity, and cross-mod interactions make it so that you can have crazy, craaaaaaazy contraptions that do some thing a block on another mod does all by itself. That's the fun in minecraft, at least for me.