I think the goal is clear and good - to abstract away the problem of different file formatting to something that users understand: I want --> FASTA for --> bowtie. I want --> Bedgraph for --> bedtools. etc.
However, I can see this abstraction having three possibly difficult issues to resolve:
1) Tools obviously change, so right now STAR takes only pair-split FASTQ files, not a single interleaved FASTQ file. This might change in the future, meaning that today's "--> STAR" format might not be tomorrow's "--> STAR" format.
2) Where two programs both support the same format (eg, in the future perhaps both STAR and Tophat both support an interleaved FASTQ), but "--> STAR" actually means read-pair-split and "--> Tophat" means interleaved due to legacy reasons, you'll get people downloading 2x as much data from your site. It isn't a 1:1 mapping.
3) "My boss was very specific and told me to get him a half-open half-closed 0-based bedgraph format with integers not floats, binned in 250bp regions -- is that bedgraph of bedops formatting?" 😵🔫
The idea of mapping formats to tools that support them is a fantastic idea -- however, it would be nice if Ensembl gave you the option to choose your data format very specifically like in example 3), but if you don't know what you want, take you to a handy look-up page that can stay updated - perhaps a grid of tools and the formats they currently support. Clicking on a tick mark in such a table could autofill the more detailed form out for you as per example 3).
Its not easy balancing the highly technical desires of some with the ease and simplicity of non-technical software others are used to, but i'm really happy to see that Ensembl is making efforts in this area :)