Lonnie's build started a trend that's for sure. As you've already noted there are a lot of variations of a single tier brewery. Probably your best option is to take a step back and ask yourself a few questions - as those will guide future decisions on modifications.
1) Do you want to do a recirculating mash? (RIMS or HERMS)
2) What are your welding and fabrication skills? If you pay someone to do the welding, sometimes simpler is better.
3) What are you planning to use for your tuns? Keggles? Pots?
The list of questions could go on - I can tell you from experience. My dad, brother and I made the decision to build a brewery months ago and we're still in the process of asking questions to complete our build.
As discgolfin pointed out - one of the simpler mods is the gas beam. Although Lonnie's is cool, it's a lot of work for probably a limited pay off. Black pipe and fittings are fairly inexpensive and readily available - if you aren't opposed to having a pipe mounted to the back - it's a popular "tweek"
Burners - do you want to go jet burner? or a different route (Banjo, Hurricane, other cast models) this will also play into your gas plumbing choices for low vs high pressure (regulators, valves, etc).
Some builds add tipping trays for the tuns to aid in cleaning.
One final thing I might throw out there is consider the height of the stand. If you have your tuns already try and mock something up with milk crates or tables, etc to get the height that are called out in the plans - we found we wanted to bring ours down several inches for a few reasons. We aren't super tall so don't need the height for one. Being able to look down into the Mash Tun and BK during brewing is nice and when the stand is too high it could be difficult.
If you spend an evening browsing through the forums, jotting down ideas you see in other builds and building a list of pros and cons of each design element - it might aid in your decision making process.
But in the end - building the Brutus 10 clone from Lonnie's plans is an excellent route as well!
Good luck and be sure to keep us updated.