With all due respect to Forrest, it sounds like you are requesting things that have already been demonstrated to be feasible in AO. Forrest is right - if you want Marathon to look modern, it should be ported to a modern engine - creating a new engine from scratch is still an effort in futility, E0 not withstanding.
The bottom line is that AO is open source and strictly the work of a very limited number of developers who do this in their spare time as a hobby. It's a lot of work and a labor of love, but you're not going to see much beyond what has already been done. It's been - what - nearly a year since Mark Levin submitted his code for a bunch of bug fixes and enhancements that still haven't made it into the main build of AO. What you ask for is not unreasonable. The balconies and bridges code has not only been demonstrated, but implemented. It really rocked, but it was one man's dream and he had to give up on it when it became all consuming of his time. He still has a website devoted to the code - at least he did last time I checked - complete with instructions on how to implement it and what remains to be done to make it fully functional. His code also included software rendering of high-res and transparent textures for older machines that didn't support OpenGL. It was the only version of AO I could use on my old Beige G3 way back when.
If you really care about this stuff, the only way you're going to see it happen is if you make it happen yourself. If you can program, write the code yourself. If not, try to hook your friends on Marathon and make it a team effort. Hell yes, I'd like to see B&B code make it to the main AO build, but I'm way too old and invested in real life to take this on myself - we need people who don't already have major life priorities to work on this. Oh, and jumping is already supported in AO. It's part of the cheat codes, but you can easily modify this in mml to assign a single key to provide jumping action. 3D objects are also already supported - what's missing there is content - creating 3D models is a major job in and of itself.