A lot of cis women struggle with this when dealing with a very feminine trans partner. Women have been sort of told, by society, that hyper feminine women are, prostitutes, sell outs to feminism, etc. Also, it can be a lot of work to present in a highly feminine manner, and not every woman enjoys doing that. All told, many cis women simply don't go all out on their presentation. Nobody says they have to - it's fine if they don't. (There is some irony that women were given a really rigid standard that they rebelled against - only to have it replaced by another rigid standard "don't be too feminine - it's a sign of repression!")
The actual answer here is that people - your wife included - need to be comfortable with who they are, as a person. Not who they are in relation to other people, but who they are. Unfortunately, in society in general, and for straight women in particular, I think, there is a tendency to define ourselves relative to others. (Especially our husbands - a lot of women, over time, subsume their identity into that of their husband's and their family. They are so busy giving to others that they simply stop being themselves - they don't have time for that!) I think this is human nature to a large extent, although it doesn't have to be this way.
Your wife's femininity didn't change one iota when you came out. I'm sure she is still all woman. However, relative to your presentation, hers seems relatively less feminine to her now. And that is uncomfortable for her, because it feels like she's somehow less than she was before, even though nothing about her has actually changed. It doesn't help that women are kind of set up by society to feel like they are destined to be "less than" others. (This is quite a cruel thing that is done to young women - they are set up to impossible standards, and when they don't meet them, they feel like failures.)
Anyway, lots of women end up feeling this way when they finally meet their trans spouse's other side.
This type of thing has led some women to call us "parodies of femininity." The thing is - nothing about our presentation in any way reflects on them - or it shouldn't anyway. You aren't asking them to present in a certain way - you are just doing so for yourself to express who you are.
I had something like this happen to me today. I met with a young woman, a therapist, who wanted to dedicate her career to working with transgender children. Well of course I'm all for that, and agreed to meet with her so that she could ask me questions about my experiences as a transgender person, because she was preparing a presentation for colleagues. She was smart, knowledgeable, and actually quite pretty. I thought she looked very feminine, in her jeans, top, jacket, and boots. Her makeup was kind of light - but she was young and pretty, and really didn't need much. She looked great!
But part way through the conversation, she kind of apologized about her nails. She told me she was trying to grow hers out, and had left them unpolished, and not well manicured. Mine were manicured and painted bright red. (I was in a dress, hose, full makeup - a fairly traditional feminine presentation, and I'm really girly in terms of mannerisms and stuff.) I never even noticed her nails, to be honest, but she sure noticed mine, and it seems to have bothered her a little. Clearly, she felt a little self-conscious about that. I don't think I did anything directly to make her feel that way, but she seems to have been just a little insecure about that. This woman had nothing to feel insecure about compared to me, trust me - she really was quite a lovely young woman, yet that's how she felt, at least a bit. Perhaps I said something completely inadvertently that she took as a criticism. I sure hope not! If I did, I sure didn't mean it.
My point is, that this woman had known me for all of 20 minutes in person, plus a like amount of time on the phone prior to our meeting. I meant very little to her, yet she reacted as she did. (I know it's a silly example.) So just imagine how much more intense such feelings could be to your wife. She's never had to compare herself to you in terms of feminine presentation. Perhaps now she does though - and that changes everything, at least relative to one another in terms of gender expression.
I also think that a lot of us judge ourselves quite harshly, and then assume others see the same flaws we obsess over, even when they don't. So perhaps your wife is doing that.
The kinds of things I think you could try to help her with this would be to point out that you think she is very beautiful, and very feminine, and that she's totally the woman in the relationship. You just dress like one sometimes - but that doesn't change the wonderful, lovely, sexy, feminine woman that she is. (I hate putting it in those terms, because they are so couched in heteronormative cis sexist ideas - but I think most straight cis people would probably understand them.)
You can also point out that she can wear jeans and a t-shirt and nobody will think she's a man. Before you look anything like a woman, I expect you need quite a bit more than that - because you in just jeans and a t-shirt would look like, well, you presenting as a male. So if you are going to try to pull this off, it takes more for you to get not nearly the effect she gets, because she has a female body, and you don't.
By the way, she may not be self-conscious about this at all, but feel you look ridiculous, or that you are a parody of women, or simply be worried that she's losing her man. In short she may be uncomfortable about this part of you on some level, even though overall she's quite supportive. She might worry that others will find out. Some negative feelings about all this wouldn't be too surprising.
Be patient - it does take some getting used to, having a trans spouse. And talk to her and ask her how she feels about all of it. Open a dialog, and hopefully she'll talk about her feelings.