After the nether mod was added, teleporter pads were still useful: they allowed easy short distance teleportation. This was useful in making structures where a player is ported into an inner room. I used it as a instant entrance to my pvp arena. Sundance used it to access his sky island house, placing people who used it in the center of his pyramid, where, if they were unaware of the trap, would promptly fall into the trap and fall out the bottom of the sky island. I feel that teleporters were no longer useful for long distance teleportation, but were very useful for short-distance puzzle and trap type teleportation. Unfortunately, nether portals are almost completely useless for that. So, the telemosaic had creative uses. Its too bad that they were removed, in my opinion.
I never got the gravel sieve to give me anything useful anyways. The chances must have been quite low. I won't miss it, as it was off focus. However, You could have easily edited the code so that it would not give minerals, but would give other items, perhaps: bones, fossils, seeds, and other items like that. IDK if that would have been worth it though.
If, with the changes, farming is profitable now, then good. It doesn't matter how long it takes, just, when its done, you should be able to collect a good deal more than you planted. A small garden should be able to produce well, though if it takes a while thats fine.
torches: good job, I thought that was weird too
Towercrane: big blah. That was a very good addition to saras survival. It allowed [limited] fly, which allowed easy construction. I think that it encourages nice buildings to be built. I do think that it is way too cheap: It should require a lot of steel, gears, metal rods, etc. It is at least as useful as a heli. But I wouldnt remove it.
the biofuel: to accomplish your purpose, you will have to make trees and wood non-burnable, or severely limit their burntime. I think that you are worrying way too much about that, but, If you want to know what actually causes people to not mine, its the moon. The ores there are very easy to get to. Either: make the moon hard to reach, and/or dangerous to make a trip to, or remove ores from it (but then what's the point? - I never go to mars, except as a novelty occasionally)
I did not find it worthwhile to go mining for coal, bc I always went to the moon and got as much coal as I needed (same with mese, diamond, etc.) I found this to be more worth the time than making biofuel. My brother made biofuel though. It requires time and effort. I think it has its place, unless you take away the moon easiness.
what to do with gravel: make a mod that adds a new vehicle that, as you ride it, if you have gravel in your inventory, then it changes the ground under the vehicle to gravel in a 3 block swath and subtracts the gravel from your inventory. Or, if you add my concrete mod, instead of using compressed cobble, use gravel in the baking recipe for concrete.
Im a fan of the rest.
P.S. I'm not playing for a while.... If/when I come back, Ill probably start over. Maybe. I hope by then the gameplay will have been updated to be both more challenging and more engaging. (more active danger, more necessity to gather resources, etc)