Overview
You have to choose your spacing and positioning very well. Samus will be off shooting auto-cancel missiles and reading your movement to get off charge shots whenever possible. After interactions in neutral, the Samus player will go for reads on your movement and reactions so they can either UpB, CC Dsmash, or grab you whenever possible. You will be wise to mix up every option choice you do against competent Samus players.
Neutral
Avoid missiles: easier said than done.
Use platforms to your advantage. Understand the pattern that they follow: Samus has to platform cancel to spam missiles so she's either shooting one closer to the ground or up high. Tether, PKF, and well timed Fair will go thru missiles. Fsmash / perfect shield will reflect them. PKF clanks them.
Use safe approaches. Don't run in blindly with magnet / Nair and use as little dash attack as possible. You'll get 0 conversions from dash attack and the move doesn't set up for anything in the MU. Magnet / Nair will get eaten by CC as well.
Other Stuff
PKF to intercept her recovery. PKT1 when she's far away off-stage to tack on some extra damage / mess up her recovery slightly. You can try going out there but it's not recommended.. As for recovering as Lucas, she can cover tether very well, so be wary of this. Bombs, Nair, etc can all intercept Lucas' tether. Her missiles can be hell offstage so don't always magnet stall right away, as magnet doesn't do anything vs missiles. This is where Fair is good to hopefully get thru missiles (2 frame active hitbox = better git gud or die).
When juggling, Uair goes thru bombs (downb), but trades with her Nair. Uair is good for comboing, and I personally believe it's better than Fair in this MU.
Concluding Notes
Read how Samus wants to shield pressure and approach.
Adapt to her missile patterns and defensive options.
Think about every move you throw at her unless you want to get absolutely messed up.
Play it safe; Lucas' risk/reward is much more potent than hers. One or two mistakes from you could equal a stock, whereas Samus' mistakes may only result in 30-40%.
At low %'s:
- Off down throw, you want to get a solid 30% or more
- Off Dair (whether it pops her up or leaves her grounded w/ no tech after the 3rd hit), you'll want to get 50% or more on Samus