: Having trouble because I can only hit by reading a shadow sneak activation and pk fire Also his uncharged water shurikens make it difficult for me to approach.
: Projectiles, mainly the bombs.
: spin dash. (the ones he can hold) I can only hit him with pk fire and shield grabbing the neutral b.
: hitting her outside of using pk fire is hard, because of the side b and grab
: too much end lag on the fsmash to reflect all the missiles.
Samus' missiles are garbage: Long startup & endlag, pitiful damage, easy to powershield, and have low priority (can be destroyed with normals and aerials), one of the worst projectiles in the game and an abomination of a move. Why would you need to reflect these again? Samus in general is a terrible character, her main weakness being her bad neutral game and poor frame data with some moves that lag for centuries, she literally has very few safe moves she can safely throw out in neutral other than zair and pivot ftilt, and she's essentially at a disadvantage even when the game has just started. Even the first hit of her Jab combo is unsafe on hit and you can shield the 2nd one or just attack back with your own jab. What also makes her such a bad character is her below average damage output, one of the worst grabs in the game, unreliable KO moves, a **** tier roll, and being a floaty yet heavy character.
: Do the Sonic's you play against spam the spindash? If so, then just shield the spindash and see what he does after. If he jumps after hitting ur shield, jump out of shield and punish with Bair or Uair. If he continues rolling on the ground, chase after him and punish his screech stop animation (like in his own games, particularly the Sega Genesis ones). Having been to the Sonic boards before and used to second him myself, I can tell you that the spin dash itself is not that great: its the mixups he has out of it that make it great (spinshots, instant spin dash jumps, shield canceled spins, etc) and Sonic in general has very poor approach options. He's a bait and punish character who's gameplan is basically "Rely on my opponent to make a mistake" or "Try to make Him Mess Up", its not a fun fight but if you stay patient and don't make too many mistakes for him to punish it becomes a bit more doable. Also on another note, Sonic's landing options are total butt and he can't really do a lot if you are directly underneath him and its easy to punish his landings and juggle him, something else you may want to take advantage of.
I must admit, I lost pretty badly to a Toon Link on FG last week and I get annoyed fighting him myself. But to bypass projectiles, learn to walk (not dash) and powershield through them to approach him and be patient. Both your grabs are pretty bad, but what Lucas can do when he finally gets in is approach with Nair and TL will have a hard time punishing it due to his bad Out of Shield Options. And if you do get a grab, you have more combo potential and kill power from your throws than he does. Not much to say here.
Used to main Greninja myself for the longest time, before I started doing better with
and made him my main while Gren's taken a back seat. Shurikens aren't that great a zoning tool and they're easier to approach than Toon Link's projectiles, ever since he got nerfed in the dreaded 1.0.4 patch the shurikens now have too much endlag to be a safe zoning tool, and I personally view that as the biggest nerf he got. Again like with TL, be patient, walk, and powershield through them if you are facing someone who plays him like a zoner, punish the endlag of shurikens if he uses them while you are too close. Shurikens are more of a long range poke than an actual zoning tool, and the charged version of it can easily be reflected by Lucas' fsmash so he should not use it that often unless its to punish your landings. Approaching with Nair is good against Greninja, he has a grab as slow as Yoshi's and generally suffers from poor OoS too, and also has meh frame data with moves that are slow to come out or aren't active for that long. I do think Greninja could be a tough one for Lucas, but not for the reasons you mention.
Not much to say about
since I have never fought her while playing Lucas. One thing I can say is to try and avoid getting grabbed and make smart use of powershielding, this character will destroy you with her combos if she gets a grab, but she is balanced because her grab itself is slow as hell and she doesn't have many other other options to threaten shields.
I dunno, Lucas is still pretty new and we don't yet know how all his MUs are going to go down, its too early to tell if you even need a secondary. I don't mean this as an insult, but it looks to me like you're being outplayed for the most part: your analysis says to me struggling more with important fundamentals or you have holes in your game with Lucas rather than with the character needing a backup, and fundamentals are always important to learn first before trying to learn your character. I think you should just be a little more patient and practice more before seeking a secondary.
EDIT: Also, in one of your other posts you said Fox has a hard time with Zamus (I'm assuming that's Zero Suit Samus you're talking about?) and Sonic. Dunno about "Zamus", but Fox definitely does not struggle with Sonic, Sonic mains themselves say Fox has the edge, actually. Fox has a better neutral game than he does with normals that are stronger, faster, and have more range; can setup into his kills (Sonic's kill power isn't bad, but he doesn't have any kill confirms), and can DESTROY Sonic the moment he goes airborne. If you do end up using him as a secondary, you should do just fine against Sonic as long as you work on your fundamentals and learn your character better.