I suggest you take a look at this question.
ffmpeg is not deprecated. You are probably receiving misleading information.
ffmpeg will work great for what you want to do. I suggest you take a second try. You can use it from PHP or Java for example and execute it through command line. It is particularly fitted for batch processing and any media-based automated task.
The option to resize in ffmpeg is -s
(see here for more info).
If you are really not convince with that I suggest you take a look handbrake which also has a command line interface for Ubuntu. Handbrake is mostly a wrapper for ffmpeg (with a GUI also).
After that there are paid options like zencoder which has a great cloud-based API. A more comprehensive list is here.
I hope you get what you are looking for. If you have any issue with ffmpeg please post your code and console output on a new question.