I don't think there is one perfect program but after working across various grade levels with GenEd, SpEd and EL, make sure you have a strong phonics component and time for the kids to actually learn how to read and spell. This should be a big focus in primary grades. For comprehension, look for a program that has the students responding constantly to text. I would say retelling, sequencing, and literal comprehension are the main skills with building beginning inferential skills.
I have found that close reading is best. Rather than reading many books or texts, read less texts but focus on actually understanding what is happening in the story and illustrations and why.
Lastly, let them read for pleasure. Give them time to pick whatever books/texts piques their interest and give them an appropriate block of time to just enjoy reading. This includes read aloud; most kids love being read to.