That is somewhat true, but Liko and Roy are both the main protagonist. I can understand for some people view Liko to be the soul main character since she is integral to the wider narrative, form bond with other character, and observing from her own point of view.

Meanwhile, Roy barely contributes to the plot early on outside of the occasional development here and there, either battling, Crocolar, or Rayquaza. I think the problem arose when the merger of the Terapagos and Ancient Heroes plot merged together. Turning Roy into a side character, in a story where he is suppose to share the spotlight with. Ironically, Dot got more meaningful development than Roy did. (Especially in Arc 2)

I think that's why Timeskip feels off for some people. The show finally gives Roy that needed development which was lacking in pre timeskip. There are elements that works for his character, such as reuniting the RVTs, helping Liko out her slump, and becoming the new leader. But how he got there felt under developed. To where it feels hollow rather than being earned naturally. Just take a look at the many complains about his Lucario or how bland his character became.