The print-centric Creative Suite applications (Illustrator, Photoshop, InDesign) can all save/export directly to PDF. They use a different software engine so Acrobat/Distiller is not involved in the process. PDF files created from all current Adobe software products comply with the ISO standard; the only difference is in the supported features - for example if you Save As from Illustrator you can choose to preserve live transparency and layers, but if you convert to PDF using Distiller you are getting what to all intents and purposes is an electronic sheet of paper. Except in very specific workflows there is no reason to bounce through a PS or EPS file.
There are some things to watch out for though - such as the 'preserve editing capabilities' option, which embeds a copy of the entire native file inside the PDF. Unless you specifically intend to pass the PDF to someone else for editing inside the same application, that option should always be turned off.
You'll have to explain what you mean by "printing funny sometimes".
Thanks for your reply. If I save or print from a PDF the letter l or two lls together look like they are bold as in "will". Its a PDF thing
Are you outlining type before creating the PDF?
Yes, Myriad pro seems to be doing it. I outlined the text then place in ID.
Is there any need to flatten text in AI seeing that PDF embeds the font if you check that box?
You should be asking these questions to whoever you're sending your PDFs to Print. Different shops have different degrees of workflows and capabilities.
With our shop, we prefer unflattened files in case we need to do any editing or special preperations for printing. Also, many RIPs these days can handle "transparent" or "un-flattened" files.