Samus has superior planking skills with z-cancels and bomb jumps. The one I face regularly just banks at edge when he's in trouble. In terms of pure gimping against a good samus, i'd say samus has easier time gimping pika offstage. At least when right at the edge.
Don't get me wrong... thunder owns, QA can recover from even the most epic of spikes, u-air spam and joltspam will pressure them to insanity.... it's just... in terms of samus realizing, "Hey, i'm just gonna plank real good," its AN AMAZINGLY HARD (or annoying at the least) FIGHT--provided they got skillz. Offstage D-air to z-ledgegrab will gimp any pika that doesn't have the non-cardinal directions down. Samus can z-air t-jolt and Pikachu at the same time if both do a full hop (no more pika autocanceled jolts). Samus can drop from ledge away from the t-jolt arc and z-air through stage and hit pika if he's grounded.
Onstage, both my samus buddy and I feel that Samus definitely is disadvantaged. Samus's still can win, its just harder for most samus's. F-throw to f-throw will work if the samus airdodges or n-airs, f-throw to upsmash will work if she doesn't. U-air is faster than d-air and on stage, pika can place u-air better. The biggest problem i run into is z-airs from far away, retreating f-airs for widening the space, and up-b's. The Samus i face uses u-tilt to kill me more often than d-tilt. SH D-air placement is a must for damage and setup for samus.
I think 60:40 may be a fair number in pika's favor. I do think that its dead 50:50 or slightly towards Samus's favor depending on stage and skilled edge-planking. Ask for stealth's input. He played me with his samus and did a fairly good job.
*i don't like near-fully charged shots, always surprises me without the massive hitlag/hitstun.... lol. With one split second of bad DI, i died at 89 damage on BF. O_O.
Edit: I'll see if i can get some vids up soon of this matchup. We do this alot since he only plays with samus.