I am intersted in replacing my current data format that I use with GTFS, but I hear and read from here and there that there are flaws in GTFS file format.
Most of the time I see that you can't somehow predict some things such as delays or some real-time stuff. They say you can't get the "whole picture" with them.
So what I am asking is there anyone more experienced with GTFS , since I am seeing them only for first time, that could have possibly used GTFS in some kind of application and could tell the problems they have faced while developing?
Maybe someone has a suggestion about a better kind of file format? Or a combination of some formats?
It's hard to say whether GTFS is a good fit or not for your application without knowing what your application's requirements are, but I can offer a few remarks.
If your goal is to provide real-time data to users you should take a look at GTFS-realtime, a complementary data format designed specifically for issuing real-time updates. For most public-transit applications, using a GTFS and a GTFS-realtime feed together does indeed give the "whole picture" about a transit network, or near enough.
In terms of GTFS itself, my main complaint is that it seems designed specifically for route-planning applications and using data in this format for any other purpose can be difficult. For example, while a GTFS feed records information about transit stops and routes, there is no requirement that each of these have a single, canonical entry—if the data spans multiple board periods, there will almost always be (seemingly) duplicate entries for each.
This doesn't matter if you're plotting a route based on where and when a person is travelling, since the links between objects ensure you'll always generate the right result. If you're starting with only a person's location and want to know, "What transit resources are available nearby?", reliably producing an accurate answer requires some contortions.