I was in the same boat as you about two months ago when deciding on my first 50 BMG rifle, and was considering the same options. Here is a digest of the homework I did:
Zel Custom T1 upper
Pros:
1. Lowest cost 50 BMG option of the rifles considered. Used rifles and some other manufacturers like Safety Harbor could be had cheaper, but for what I could find had more of a hit-or-miss reputation from Zel. The issues I did hear about regarding Zel had to do with reliability and never safety, and all were handled expertly by Zel's customer service.
2. Lots of customization options available regarding barrel length, brakes, and lower configurations.
Cons:
1. While sold as a "drop on" lower, it really isn't. You can use an existing AR lower with some modification (removing the bolt catch), but you would likely have to upgrade to a stronger hammer spring. Realistically you would be better served to build on a dedicated lower, preferably a single shot so you don't have an awkward mag well.
2. While it is cheaper to buy, the resale is not as good. It is unlikely to get a full return on your investment if you need to sell.
Zel Custom T2 upper (mag fed)
Pros:
1. Same as above, along with the addition of a magazine fed capability
Cons:
1. Same as above
2. Reports that the side loading magazine configuration leads to the rifle pulling toward the heavy side due to the magazine's weight
Armalite AR50:
Pros:
1. Widely regarded as the most accurate of the out-of-the-box 50 BMG rifles.
2. Relatively cheap for a complete rifle.
3. Decent resale value
4. Low recoil
5. Most adjustable rifle in terms of stock/cheek weld
Cons:
1. HEAVY
2. Price becomes less favorable vs the primary competitor (M99) once you factor in the additional things the M99 comes with
3. Very long rifle-- can make storage and transport difficult
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