Eph 3:21 is often used as a “proof-text” against the Latter-day Saint view of the Great Apostasy. I discussed briefly this passage here, but I encountered the following comment on this verse from two other LDS apologists which hits the nail on the head:
Another passage, Ephesians 3:21, “Unto him [the person who glorifies God; see verses 19-20 for the context] be glory in the church by Jesus Christ throughout all ages, world without end. Amen.” What Paul appears to be saying here is that those followers who “do exceedingly abundantly above all we ask,” (verse 20) will have infinite glory, without time or spatial constraints (“throughout all ages, world without end”). Paul is explaining the wonderful state of this glory, not the survival of the Church. It is this glory that is the subject, and not the church. In dealing with anti-Mormons, one must be careful about such subtle changes of subject. (Alan Denison and D.L. Barksdale, Guess Who Wants to Have you for Lunch? A Missionary Guide to Anti-Mormon Tactics & Strategies and How to Deal with those Who Have Been Influenced by Them [Foundation for Apologetic Information & Research, 2002], 30)
