Did Christ Deny Paul's Prayer?

I'm also of the opinion that Paul didn't get what he prayed for. If he had gotten it, his second and third prayers would have been unnecessary. In fact, Paul himself seems to state fairly directly that God declined to grant Paul's request. Paul, of course, found reason to be thankful anyway, recognizing that God's grace was a greater gift than physical health (or whatever the "thorn" impaired). This also accords with normal Christian experience: we frequently don't get what we ask for in prayer.

As you indicate, this can be a troubling realization. After all, the Bible seems to indicate in more than one place that our prayers certainly will be answered affirmatively (e.g. Matt. 21:22; Mark 11:22-24; John 14:13-14; 15:16; 16:23-26; Jam. 5:14-15). I think, however, that there are a couple of things that come into play that we often fail to consider when we interpret these passages, and that in reality these passages do not promise that all our prayers will be answered affirmatively.

First, none of these passages is actually a "promise." They are all offers of blessing, but none of these offers is made in the context of an oath, a covenant, a promise, sworn fidelity, or any other such qualifier that would bind God to fulfill every petition brought to him. When God says things, they do not become certainties merely by virtue of the fact that God cannot lie. Rather, God has varying degrees of intentionality when he offers blessing (and when he threatens curses). As shocking as it may seem, what he says need not actually come to pass as he states it. Rather, God is free to change his mind (e.g. 2 Sam. 12:13-22; Jer. 18:1-10; Jon. 3:4-10). Only when he actually promises (by covenanting or otherwise explicitly swearing an oath) is something certain to happen. Thus, God may often answer prayer affirmatively, and these offers may (or may not, see below) indicate his bias to answer them favorably, but God is not bound to give us what we request.

Second, most of the statements that prayer will be answered affirmatively are made directly to the apostles, and not to the Christian population at large (e.g. Matt. 21:22; Mark 11:22-24; John 14:13-14; 15:16; 16:23-26). While I believe that these passages extend great hope that God loves all believers and is favorably disposed to give us what we ask, I also believe that the stronger assurance they offer directly was not intended for all believers. Rather, as I understand the contexts of these passages, they seem to indicate a special apostolic gifting for ministry. It appears to me that Jesus is telling the apostles that their prayers especially will be answered affirmatively, and that this gift is given in order to empower their ministries when Jesus is gone and to defend their authority. Their prayers in particular are generally answered affirmatively in order to validate their message as truly being from God. Along these lines, "in my name" (John 14:13-16; 15:16; 16:23-26) is either a request that a prayer be granted for the sake of Christ, or (more probably in my opinion) an indication that the prayer is offered by one to whom the authority of Christ has been delegated (cf. "until now you have asked for nothing in My name"; John 16:24). Thus, in the book of Acts, for example, we see great power in the prayers of such people as John, Peter and Paul -- power which exceeds that of those who are not apostles. We do not see people carrying the sick to see the nearest Christian in the hopes of healing, but rather being carried to the apostles (e.g. Acts 5:12-16). I believe this special attention to the apostles' prayers was intended to make people trust their message and to respect the authority that Christ had delegated to them. The rest of us have not been entrusted with this authority, called to the office of apostle, or given apostolic gifts.

In the case of James 5:14-15, notice that it is the elders who must pray collectively, and that their prayer must be offered in faith. The elders are the ruling body of the church, and as such are collectively entrusted with greater authority than other believers. While this is not the same as apostolic authority, it may be an indication that this is a special case of intercession in which God grants special favor to the prayers of the elders in order to validate their ministry as well. Moreover, this elevated assurance is given only for prayers offered in very specific circumstances: a believer is dying because God is judging him for his sin, the sinner confesses to the elders, and the elders intercede on the believer's behalf. The greater assurance of healing is not attached to the prayers of all believers, but only to the prayers of the elders collectively.

Believers at large should have great confidence in their prayers, knowing that God loves them and that he genuinely desires to do them good (e.g. Matt. 6:5-6; 7:7-11). But we should not presume that he is somehow obligated to give us what we ask.