I would favour Emelianenko in a ring or cage. I think his hand traps and hand fighting would do a great job of neutralizing Velasquez's jabs, and just harassing them in general, the wrists and hands, which is his main entry/threat of coming in and cutting off/initiating offence (I see Velasquez having much more problems in a ring, where I'd favour a prime Filipovic over him too). The hand traps and parries would also help him in landing bigger power shots than Velasquez. He's proficient with back-step punching and Velasquez tends to get overaggressive and shows some bad defence coming in at times (JDS was hitting him with some good shots at the start of their 3rd fight and in other similar sequences), which I think he'd capitalize on - showed great kicks in his career, counter low kicks, high kicks, but he didn't use them as much as he should have.
Some of the positioning problems Velasquez has when he comes in is his head sometimes is really outside his feet or really upright (open to straights), his back not always straight, the knees sometimes dramatically bent in close range, or having the back bent but not the knees. His feet should also stay somewhere near shoulder width apart the majority of the time but if you watch him cutting off, he's in some bad positions that JDS and even Kongo capitalized on. Velasquez sometimes comes straight in with his rear right there to be hit, not offline or lowered, and can get caught by a nice straight counter (a reason I think a prime Filipovic would do better than JDS with his side stepping and back stepping left straights). It's generally most defensively sound to make sure the lead hip and shoulder are the closest things to the opponent and the first to enter range, but he makes mistakes with his rear positioning. Although there are some advantages to having the weight and head farther forward provided he shouldn't stand like that in range because a guy like Emelianenko would pick up on that rather quickly (he's very intelligent about the fight game and I'd recommend reading his book if you haven't, very in-depth about his striking, grappling, workouts, etc.; you could tell he wasn't the same guy from the Sylvia fight). He also has a tendency to duck his head and take his eyes off the target which could be very deadly against some of his counters.
Emelianenko had fantastic footwork, head movement, counter combinations (which JDS lacks), and the speed to at least match the work-rake and shots. I think he was a better striker and grappler tbh, but Velasquez's level changes and wrestling would be tough to deal with, for some of his counters too. His dirty work in the clinch would be interesting too but Emelianenko's own great work in the clinch and judo (and sambo base) would make it difficult for him to get much going, I think. The ground fighting would be very interesting though, and I think that's Velasquez's best shot and his cardio/relentlessness would be there obviously. Emelianenko's the most complete HW ever and I definitely see him fighting well against the pressure pace style of Velasquez.
Emelianenko didn't have the volume g&p of Velasquez but he had more calculated and technical ground striking, cleverly used the threat of submissions and positional changes to create openings for his strikes (like striking on the pass), tricky baits to open up strikes and subs, etc. He masterfully mixed his strikes with his grappling while changing and gaining positions of leverage above his opponent, either by posturing down and up - from various positions, getting underhooks, transitioning, trapping their legs to force them into bad positions like giving up their back, getting to his knees, using his knees to neutralize wrist controls, controlling portions of their upper body, etc. He doesn't waste energy on it, nor did he have the work-rate of Velasquez. It's different styles but both have great top games. Velasquez's BJJ is fairly underrated but I don't think he'd be able to threaten Emelianenko with subs, cut through his defence, get dominant positions (like his back, or even advance past half guard), etc. Emelianenko had great escapes anyway, and I believe he'd find openings off his back if he's put there to get back up, sweep, threaten with subs, or get into more favourable positions. Velasquez might also fall for some of those submission baits he liked to use. Maybe Velasquez has a great guard (we haven't really seen him there) which he could stalemate from but I doubt Emelianenko would have trouble with it considering what he did in a peak Nogueira's guard.