3 ways to skin a cat. All seem to work. The biggest problem with the long to short program, is that most don't tailor that program to fit their athletes current developmental state. The biggest problem with the short to long program is that most don't give it the time required to work. Ends to middle works well for both short term and long term, but it's biggest drawback is the athlete tends to get overworked sometimes, it's biggest advantage is you can tell which way needs to be worked more.
Generally, quicker gains are seen with Long to Short, Slower gains with short to long, and intermediate paced gains are seen with ends to middle in terms of 400m time. If you have only 4 weeks to prepare someone for 400m dash then Long to short is good, if it's a HS type season then ends to middle probably is the best, but if you have a year round training program then short to long would fit better as the yearly training volume should help give the endurance boost required.
Ends to middle and short to long (year round) produce the best all-around sprinters.