A lot of great suggestions....
Some thoughts, you can do a theme, such as crib linens/towels & washcloths/blankets/clothes - if the shower is kept small, these should fit in a suitcase to go back. She'd just need to bring or borrow an empty suitcase with her to go back.
If you don't want to specify what type of gift, she can always return all the big stuff and repurchase at her local store? A bit of a pain, but an option. (Although, I know how busy I am and it would be a little disheartening to know I wasted my time even bothering....)
Gift cards can sometimes be hard because some people actually have coupons that they would've used on the larger items. But then again, they can just do a gift card for what they planned on spending.
Really, shipping isn't always horrendous and maybe some immediate family may help absorb the cost by contributing...but I wouldn't ask everyone to do so. You could certainly put a note with the invitation that the couple welcomes gifts shipped to their home, if the giver chooses to do so. I think most people attending realize that the gifts will have to get there, anyways!
I have to second the book idea over a card - help build up her library for her baby!! There's a poem (search online) which is good to include to let guests know to sign their name to a book instead of a card.
Oh, another idea would be to have a scrapbook party/shower where each person customizes a page in a scrapbook that mom will get to take home. You can have themes set aside for each page (Mommy & me, Daddy & me, grandparents, first bath, one month, two month, etc., or a letter of the alphabet for each page with a word or animal to go along with it Adorable, Baby, Cutie...Alligator, Bee, Caterpillar...) - get the paper and embellishments and set aside for each theme then people can choose or draw a name out and design that page, leaving a spot for a picture to be put in later.
Intimate showers are a lot of fun - you can keep it traditional, plan a pampering type thing, or think way outside the box. I do like the ideas in creating a mommy's advice book. I've seen this done as the guestbook for the shower or as pages where people can write it out at their seat and are later collected.
Best wishes! Congrats to your sister!