And again recommending Maker, but: Maker is not a graphical tool, it is a pipeline of tools to create consensus gene calls. That is a good start for an automatic draft annotation imho, but not sufficient in the long run. Good genome annotation requires manual curation by dedicated experts, possibly with integration of data from experimentalists. To aid manual curation, set up a genome browser, e.g. Gbrowse2, Jbrowse, or best a complete model organism database. It will give you the advantage of storing your genome annotations in a consistent way. Having a web-based genome browser will enable biologists for collaboration. Collaboration is the key.
In the genome browser, create tracks for the different gene-predictions (Maker, Augustus, Genemark), a track for the alignments of ESTs, RNA-sequencing coverage, re-sequencing, conservations scores and maybe blast hits to other related organisms and what not. Also run tRNAScan-SE to predict tRNA, afaik Maker doesn't do this (does it Zev?). Now, work with this annotation for a while, together with the biologists, to see if they e.g. find the genes they are interested in in the annotation. They should provide suggestions for improving the existing annotations.
If you intend to initiate a real curation process of your genome, I recommend to visit something like the Biocuration conference to see how curators work. (Curation is a fulltime job it seems, a very important one, but possibly not the most attractive work for a bioinformatician). In the proceedings of Biocuration there were a few consensus gene callers; also approaches for community annotation are described there. For arriving at a high quality, reliable and stable annotation, I expect that it takes a few years, even with a bunch of experts working on the genome.
Counter argument: Hey, this is so old fashioned. This guy takes it way too seriously, just take the draft annotation and be happy...
You are correct Michael, Maker does not run tRNAScan-SE.