More specific "engine type" by model
 

I think it would be good if the engine type was a little more specific than "Gas H4" with "1.8L 4-speed auto" for example.

First, I don't know what H4 means, other than 4-cyl I'm guessing. I'm looking at the Toyota Matrix and the current generation is offered in many different engine configurations:
1.8L 4-speed automatic
1.8L 5-speed manual
2.4L 4-speed auto AWD
2.4L 5-speed auto
2.4L 5-speed manual

When I'm looking at the Matrix on Fuelly it is impossible to tell what engine configuration each is and each offers slightly different EPA fuel efficiency.

This is a frequent request, most recently here: More accurate detail tracking? I won't rehash all of the arguments from that thread, but to summarize: we want our site to be easy to use and we don't want to scare away people who might find that level of detail confusing. We think there are large groups of people who don't know what their engine displacement is, let alone what engine displacement is. And we don't want the site to be unfriendly to people who aren't car enthusiasts.

We know this drives people who are car enthusiasts crazy. They see the minute differences, they want to sort by those differences, and have fun with more data. We absolutely understand that. Our goal however is to get the most number of people tracking their data as possible. And we feel like asking for too many details upfront will deter people from tracking, period. We know that means fuzzier data and we're ok with that.

I think there's a place on the web for a site that caters to people who want that level of detail. In fact, the EPA website has its own fuel tracker, and you do need to know/select your engine displacement and many other details before you begin. That might be a place to look if you're looking for more detail in real world reporting.

Here are some descriptions of the engine codes we use: What do the engine type abbreviations such as L4 and V6 mean?

What I would think is just enter your specifics in your cars cars description. Like on my Del sol there are three engine options, the d15,d16 and the b16, so I just entered that it was a d15 with a 5 speed manual. I dont know that it is searchable but anyone who is curious enough to click on the car will see it.