I think the layout is rather good. Some quick suggestions:
I’d make the headline smaller and/or if available a type with more character for this purpose.
The figures of the footnotes in the margin stand too far apart.

Perfectly reasonable choices for this subject matter — Myriad and Chaparral. And the grid you have set up is working well for this document.

Have you considered ragged right alignment? The narrow columns especially could gain from that approach — you wouldn't have to struggle with gaps between the words, such as “e 2009, Guida web” in the far right column on page 1.

Looking at page 4, the condensed Myriad text that appears under “I progetti in atto e gli sviluppi previsti” is a little overwhelming. I understand the constraints you outlined, but this block does seemed crammed. Any possibility of letting that particular info breathe a little?

On p3, the "Sistemi informativi" at the bottom looks confusingly like the "Gli output e i risultati" subheading above. Should it be moved under the line (or should the line be extended over it)?

Thank you very much for the comments so far. They’re very thoughtful and helpful, and I will try to implement the suggestions as soon as possible.
Juergen: Do you think I should reduce the white space between headline and body too? As for typeface with more character, I see what you mean, but our titles tend to be on the longish side, with very long words (things like “esternalizzazione” or “tossicodipendente”) and that’s one of the reasons why I choose Myriad Condensed. But maybe a Smaller size Chaparral can work.
As for footnote references, you’re absolutely right. And that will teach me to trust more my eyes and less measurements. I think I will need to find a way to align the reference numbers to the right (see page 5, for example).
John: I too would prefer ragged right for footnotes. Problem is, I’m not very good at tweaking hyphenation & justification settings, and, with the defaults, ragged text has many more line breaks than justified text.
As for the Myriad text, you’re right. I need to find a different solution for boxed text, and use Myriad Condensed just for real tabular data and headings.
Craig: I see what you mean. The line don’t extend across the page in order to give a stronger visual clue that (especially in odd pages) “Prospettive Sociali e Sanitarie” isn’t directly related with the column above it. I will experiment different solutions (do you think that changing the appearance of “Sistemi informativi” will suffice? Suggestions on how change it?).

Riccardo,
Yes, if you are reducing the size of the Myriad headline i would also reduce the white space beneath. And ragged right setting for the footnotes would look definitely better; the column is too narrow for a decent justified setting in this type size.

I attached a new revision (pssRev-A.pdf), which tries to address the issues raised by your comments. Any better?

Yes, in my opinion, you have improved the layout.

Good improvements.
That box on p4 still looks quite congested and overwhelming, thought the font change was a move in the right direction.

Good improvements. Some more suggestions:

Firstly, I would keep the figures a bit further away from the footnotes. You might almost double the space that is there right now.

Secondly, I suggest using the proper OpenType superscript figures that come with Chaparral (at least with the version I have licensed) for reference numbers. In the footnote formatting options, you will have to set the position to ‘Normal’ and apply an appropriately defined character style.

Thirdly, small caps would probably look good in the ‘Bibliografia’ for the names in front of the brackets and contribute to structuring the list. Maybe you want to try lining figures in this section, which tend to look less busy.

I'm not sure how much attention people usually pay to vertical rythm, but I would've set the leading for each level in your hierarchy "in beat" with your body leading, and also aligned the side notes to the bottom line.

Yes, the footnote figures are too close now, also too big?

Thank you very much all. I'm digesting the new inputs and will produce a new revision as soon as possible!

This is a nice design for this sort of publication. I think it reads well while being very efficient and professional in appearance. However, the color of the standfirst looks a little light to me, especially if this will be printed offset. Is it Chaparral Light Italic? With the extra leading there, you may find Italic Subhead (non-Light) to give better color.

I agree with Frode about the leading - the heads seem a little out of rhythm with the text, especially when they fall at the top of a column. And I would suggest using oldstyle figures for the numbering of the notes in the margin and agree with R. that it would be better to use true superscript figures (lining) for the note reference numbers in the text. In the bulleted list, the space between the bullets and their text is a little large, relative to the size of the bullets. Perhaps move the bullets to the right some? Also, I would probably put nota 12 above the bibliografia.

Why number the notes with old style figures? Think hierarchy!

Thanks again, later I will post the revised layout. In the meantime, some notes:
About proper superscript figures: absolutely! That was just an oversight from my part. Proper superscripts were one of the reasons I choose Chaparral in the first place (even if maybe I will need to make them a little bigger than default). I just would have liked them linked to the superscript feature of InDesign...
About oldstyle figures for the numbering of the notes, I'm with Frode on this one: I think in this case lining figures, being more consistent, work better as visual markers.
About subheads alignment: They are (sort of) aligned:

Frode: Why number the notes with old style figures? Think hierarchy!

Perhaps this is a European vs. Anglo-American difference. It looks odd to me because the first line of the note as a whole, including its number, forms a single element of text, and varying figure styles within that element seems inconsistent without actually conveying anything to the reader. I probably wouldn't use lining figures for the note numbers unless the notes used lining figures altogether.

I've attached a new iteration. Here's the changelog:
- Tried a different approach to main headlines.
- For the standfirst, as much as I would like to use Chaparral's opticals, unfortunately they're not included with Adobe CS3. I tried the non-light italic. Better colour?
- Aligned footnotes to the bottom, eliminated any other alignment with the baseline.
- Slightly wider space between text and reference numbers of notes.
- Also applied Semibold to reference figures and made them a tiny bit smaller than text.
- Proper superscript figures for in-text reference figures (too small?).
- Tweaked a bit more the dreaded text box at page 4.
- Reduced space between bullets and text, used bold bullets, also moved a bit to the right.
- Used small caps for bibliography's authors. Decided against lining figures, especially because of small caps ;-)

As for David (archaica)'s suggestion about placing notes above bibliography, it sure make more sense (the notes pertaining to the main text, etc.), but I preferred to leave the more visual clue of notes always being placed on bottom right.

I like the color of the standfirst better this way. It has lost some delicacy, which I guess is what you used the Light Italic for, and which maybe the Subhead optical could have retained. But given the constraints, I prefer the new version. Again, this assumes offset printing. For digital printing, where type tends to gain weight rather than losing it, the Light might be OK.

The reference numbers in the text for the notes look much better. However, noting your concern about "aging readership", if you think they're too small you could cheat by using the numerator figures rather than the superscript figures. They're a little bigger and lower but will still be easily understood by any reader as superscripts.

Thanks again, David. Yes, presently the journal is printed offset, and your comments are very apt.
I will also do some testing with superscripts size.
Anyone about the new style for the main headings?