I'm not as heavy as BuildCraft user, nor was I during its height, but there are a few things that come to mind :
* Documentation. I don't expect a Lexica BuildCraftia, but there are more tools available for in-game documentation now than there were before. Even if you don't include the full recipes on paper, at least giving people an idea of what things exist and what don't would help a huge amount. A list of the engine types and fuels the handle, and lists of each type of pipe and their primary characteristic, and one of the major machines could come in a fairly small page count. Useful both for people coming to the mod fresh, and for those who're returning to see the new stuff. It's possible to overdo in-game documentation and just swamp people (Reika's mods!) but I think you're way too far on the other end of the spectrum right now. As a short-term fix, expanding on tooltips alone could help with the more specialized piping like Emerald/Lazuli/Dialazuli.
This is a particularly severe issue for BuildCraft because the online wikis range heavily in quality, and in many cases are out-of-date.
* Smoother progression curve. Kinesis pipes already handle this reasonably well, but item pipes and especially item pipe engines don't really follow a normal progression path. There are very few blocks that can produce enough material to need or even want Stirling or Combustion Engines attached to wooden item pipes, and most (all but Enderchest?) of those auto-eject items. As a result, item pipe engines go directly from wooden engines to the autarchic gates, and the lowest-level Autarchic Gate requires serious power and diamond infrastructure, and Ender Pearls that BuildCraft doesn't make any easier to gather. Adding upgrades to wooden engines that allow for more compact builds before the laser table would probably smooth this out, even if they can't do any logic or internal redstone power.
As a lesser matter, there also aren't many BuildCraft machines that match the fluid pipe curve as its established, either in BuildCraft alone or in the BC + RC + Forestry ecosystem. Devices tend to take much less than stone fluid pipes can handle, or require multiple gold pipe hookups. It might be intended to operate like the Kinesis progression curve, where higher-tier piping makes up a backbone for a spoke-based distribution system, but the lack of feedback for an overpressured fluid pipe means it's harder to troubleshoot than Kinesis pipes.
* Quick-and-dirty fluid transport. Oil's really hard to make into a usable form in BuildCraft without a portable tank equivalent, because unless the oil patch is very close to a base or quarry location it's simply too much of a pain to exploit it. It is much, much easier and more effective to move a batch of charcoal than to refine a few buckets of Fuel. Other mods include fluid transport, but many overrun base BuildCraft functionality (ThermalExpansion most obviously) at the same time.