I'm really happy with my conversion. Wasn't hard to do, has considerably more power than most factory bikes and was massively cheaper.
Many of the factory bikes have proprietary designs or parts and don't let the user change the programming. Conversion kits typically allow one to mix and match batteries. They allow converting back to a normal bike or swapping the electronics to a different bike. Conversions do tend to be more hands on, whereas factory bikes often require repairs at a bike shop.
The wires everywhere is a valid complaint. I hate cable and wires, but seems like a small price to pay for everything the conversion gives you. Haven't had any issues with loose wiring so far. Some of the oversized tubing used in factory ebikes to hide stuff is not exactly pretty either.
There are a number of kit vendors out there. The Bafang stuff is highly regarded, lots of people using them, unbelievable amounts of information available on line with lots of aftermarket support/parts available. Bafang allows the user to custom tune things like power output, speed limits, etc. make for a much improved bike. I simply downloaded a tune from someone else, very happy with how it is set up.
I highly recommend a Bafang conversion on an older bike.
By the way ebikes don't really need anything special in terms of brakes. Standard rim brakes, as long as they are set up and adjusted correctly, are more than sufficient. I have V brakes on my conversion that are very responsive.