The Magix cabinet is smaller; could help in a tight phone closet. In theory, the metal cabinet could help with self-cooling a little better. In practice, cards are a little harder to insert/remove than the Legend packaging.
The punch-down-ability of the TDL cards is obviously a matter of choice, but using that Amphenol connector makes it easier for punch-down, and you can just insert a "harmonica" if you like plugging in patch cables. It's harder to go the other way when the station card only has jacks. (Octopus cables work, but are messier.)
I've heard of fewer reliability problems with the 44xx TDL series of phones than the MLX phones.
Clearly, Magix will get another software release, and perhaps another new circuit board or two. As is obvious, no more Legend features. But as long as Avaya is advertising the upgrade path, we can expect at least support for migration of MLX phones and some circuit cards; this has been a plus in the Merlin series now for almost 20 years - being able to bring phones along to the next generation.
For low-budget operations, older Legend parts and phones will stay a lot cheaper. eBay prices for MLX phones have dropped considerably in the last year. You can get MLX phones for under $25 that are in good working order. Sometimes the phones are so cheap I have to wonder how many are just stolen - what companies are really dumping perfectly good MLX sets?
A few of us nostalgia nuts still love the look of the old classic Merlin phones, which only work on Legend and earlier. They are still readily available, though I've noticed fewer dealers refurbing them. Perhaps only 4 more years of practical life.