Makoto time jumped several times in order to avoid Chiaki's confession she also went out of her way to avoid him after she discovered his feelings. To me, this is not the behaviour of someone who is in denial about liking someone. I didn't get how she went to such an extreme length of avoiding him to liking(loving) him at the end, seemed so forced to me, what do you guys think?
From Makoto's use of time travel it's shown her aims are to try to keep her groups dynamic the same. She doesn't really want anything to change, she wants their current situation to last forever, as friends, hanging out playing catch.
So it's likely she does indeed have these feelings, but was in denial, ignoring them because she knew it would upset the group.
Eventually she realises that she can't really keep that up, especially once she realises the time travel ability is limited. So her true feelings come forth.
Anyway, that was my interpretation, I think it's fairly accurate and hope it satisfies you.
Ps. You could probably claim lots of other things also played a part, such as seeing her best friend with him (She could have become jealous, helping her realise her feelings)